Kuan-Hao Chao
| Snapshot Date: 2026-05-24 13:45 -0400 (Sun, 24 May 2026) |
| git_url: https://git.bioconductor.org/packages/sangeranalyseR |
| git_branch: devel |
| git_last_commit: f6375ae |
| git_last_commit_date: 2026-05-05 23:58:14 -0400 (Tue, 05 May 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-25 11:36 -0400 (Mon, 25 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4937 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4639 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1895/2379 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sangeranalyseR 1.23.0 (landing page) Kuan-Hao Chao
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for sangeranalyseR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the sangeranalyseR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sangeranalyseR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: sangeranalyseR |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings sangeranalyseR_1.23.0.tar.gz |
| StartedAt: 2026-05-25 04:07:07 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 04:14:38 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 451.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sangeranalyseR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:sangeranalyseR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings sangeranalyseR_1.23.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/sangeranalyseR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-25 08:07:07 UTC
* checking for file ‘sangeranalyseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sangeranalyseR’ version ‘1.23.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘sangeranalyseR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
installed size is 8.6Mb
sub-directories of 1Mb or more:
data 1.0Mb
extdata 5.5Mb
libs 1.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SangerAlignment-class 36.794 9.772 43.660
SangerContig-class 8.795 2.384 10.492
SangerAlignment 8.334 2.623 10.178
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
sangeranalyseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL sangeranalyseR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘sangeranalyseR’ ... ** this is package ‘sangeranalyseR’ version ‘1.23.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c peakvalues.cpp -o peakvalues.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o sangeranalyseR.so RcppExports.o peakvalues.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-sangeranalyseR/00new/sangeranalyseR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '==' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sangeranalyseR)
sangeranalyseR.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(sangeranalyseR)
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following object is masked from 'package:utils':
data
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: DECIPHER
Loading required package: sangerseqR
Loading required package: pwalign
Loading required package: stringr
Welcome to sangeranalyseR
>
> test_check("sangeranalyseR")
INFO [2026-05-25 04:10:43] #################################################
INFO [2026-05-25 04:10:43] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:10:43] #################################################
INFO [2026-05-25 04:10:43] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:10:43] ========================================================
INFO [2026-05-25 04:10:43] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:43] ========================================================
INFO [2026-05-25 04:10:43] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:10:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:44] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:10:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:44] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:10:44] >> The number of reads detected: 2
================================================================================
Time difference of 0.05 secs
SUCCESS [2026-05-25 04:10:46] ==========================================================
SUCCESS [2026-05-25 04:10:46] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:46] ==========================================================
INFO [2026-05-25 04:10:46] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:10:46] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:46] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:46] ========================================================
INFO [2026-05-25 04:10:46] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:46] ========================================================
INFO [2026-05-25 04:10:46] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:10:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:46] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:46] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:10:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:47] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:10:47] >> The number of reads detected: 2
================================================================================
Time difference of 0.03 secs
SUCCESS [2026-05-25 04:10:49] ==========================================================
SUCCESS [2026-05-25 04:10:49] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:49] ==========================================================
INFO [2026-05-25 04:10:49] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:10:49] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:49] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:49] ========================================================
INFO [2026-05-25 04:10:49] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:49] ========================================================
INFO [2026-05-25 04:10:49] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:10:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:49] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:10:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:50] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:10:50] >> The number of reads detected: 2
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:10:51] ==========================================================
SUCCESS [2026-05-25 04:10:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:51] ==========================================================
INFO [2026-05-25 04:10:51] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:10:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:51] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:51] ========================================================
INFO [2026-05-25 04:10:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:51] ========================================================
INFO [2026-05-25 04:10:51] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:10:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:52] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:10:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:52] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:10:52] >> The number of reads detected: 2
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:10:54] ==========================================================
SUCCESS [2026-05-25 04:10:54] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:54] ==========================================================
INFO [2026-05-25 04:10:54] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:10:54] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:54] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:54] Aligning consensus reads ...
SUCCESS [2026-05-25 04:10:54] #############################################################
SUCCESS [2026-05-25 04:10:54] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:10:54] #############################################################
INFO [2026-05-25 04:10:54] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:10:54] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:10:54] >> 1 forward reads.
INFO [2026-05-25 04:10:54] >> 1 reverse reads.
INFO [2026-05-25 04:10:54] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:10:54] >> 1 forward reads.
INFO [2026-05-25 04:10:54] >> 1 reverse reads.
INFO [2026-05-25 04:10:54] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:10:54] >> 1 forward reads.
INFO [2026-05-25 04:10:54] >> 1 reverse reads.
INFO [2026-05-25 04:10:54] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:10:54] >> 1 forward reads.
INFO [2026-05-25 04:10:54] >> 1 reverse reads.
INFO [2026-05-25 04:10:54] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:10:54] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:10:54] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:10:54] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:10:55] #################################################
INFO [2026-05-25 04:10:55] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:10:55] #################################################
INFO [2026-05-25 04:10:55] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:10:55] ========================================================
INFO [2026-05-25 04:10:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:55] ========================================================
INFO [2026-05-25 04:10:55] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:10:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:55] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:10:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:55] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:10:55] >> The number of reads detected: 2
================================================================================
Time difference of 0.03 secs
SUCCESS [2026-05-25 04:10:57] ==========================================================
SUCCESS [2026-05-25 04:10:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:57] ==========================================================
INFO [2026-05-25 04:10:57] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:10:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:57] ========================================================
INFO [2026-05-25 04:10:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:57] ========================================================
INFO [2026-05-25 04:10:57] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:10:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:57] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:10:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:57] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:10:57] >> The number of reads detected: 2
================================================================================
Time difference of 0.03 secs
SUCCESS [2026-05-25 04:10:59] ==========================================================
SUCCESS [2026-05-25 04:10:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:10:59] ==========================================================
INFO [2026-05-25 04:10:59] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:10:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:10:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:10:59] ========================================================
INFO [2026-05-25 04:10:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:10:59] ========================================================
INFO [2026-05-25 04:10:59] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:10:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:59] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:10:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:10:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:10:59] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:10:59] >> The number of reads detected: 2
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:11:00] ==========================================================
SUCCESS [2026-05-25 04:11:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:00] ==========================================================
INFO [2026-05-25 04:11:00] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:11:00] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:00] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:00] ========================================================
INFO [2026-05-25 04:11:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:00] ========================================================
INFO [2026-05-25 04:11:00] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:00] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:11:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:00] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:11:00] >> The number of reads detected: 2
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:11:02] ==========================================================
SUCCESS [2026-05-25 04:11:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:02] ==========================================================
INFO [2026-05-25 04:11:02] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:11:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:02] Aligning consensus reads ...
SUCCESS [2026-05-25 04:11:03] #############################################################
SUCCESS [2026-05-25 04:11:03] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:03] #############################################################
INFO [2026-05-25 04:11:03] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:03] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:03] >> 1 forward reads.
INFO [2026-05-25 04:11:03] >> 1 reverse reads.
INFO [2026-05-25 04:11:03] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:03] >> 1 forward reads.
INFO [2026-05-25 04:11:03] >> 1 reverse reads.
INFO [2026-05-25 04:11:03] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:03] >> 1 forward reads.
INFO [2026-05-25 04:11:03] >> 1 reverse reads.
INFO [2026-05-25 04:11:03] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:03] >> 1 forward reads.
INFO [2026-05-25 04:11:03] >> 1 reverse reads.
INFO [2026-05-25 04:11:03] >> 8 reads created from FASTA file.
DEBUG [2026-05-25 04:11:03] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:03] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:03] ========================================================
INFO [2026-05-25 04:11:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:03] ========================================================
INFO [2026-05-25 04:11:03] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:11:03] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:03] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:11:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:04] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:04] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:04] >> The number of reads detected: 2
INFO [2026-05-25 04:11:04] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.03 secs
SUCCESS [2026-05-25 04:11:05] ==========================================================
SUCCESS [2026-05-25 04:11:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:05] ==========================================================
INFO [2026-05-25 04:11:05] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:05] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:05] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:05] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:05] >> For more information, please run 'object'
DEBUG [2026-05-25 04:11:05] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:05] ========================================================
INFO [2026-05-25 04:11:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:05] ========================================================
INFO [2026-05-25 04:11:05] >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-25 04:11:06] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:06] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-25 04:11:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:06] >> 'Achl_RBNII384-13_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:06] >> 'Achl_RBNII384-13_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:07] >> The number of reads detected: 2
INFO [2026-05-25 04:11:07] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:11:08] ==========================================================
SUCCESS [2026-05-25 04:11:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:08] ==========================================================
INFO [2026-05-25 04:11:08] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:08] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:08] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:08] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:08] >> For more information, please run 'object'
DEBUG [2026-05-25 04:11:08] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:08] ========================================================
INFO [2026-05-25 04:11:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:08] ========================================================
INFO [2026-05-25 04:11:08] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:11:09] >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:11:09] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:11:09] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:09] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:09] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:11:09] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:09] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:09] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:11:09] >> The number of reads detected: 2
INFO [2026-05-25 04:11:09] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.04 secs
SUCCESS [2026-05-25 04:11:10] ==========================================================
SUCCESS [2026-05-25 04:11:10] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:10] ==========================================================
INFO [2026-05-25 04:11:10] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:11:10] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:10] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-25 04:11:10] >> For more information, please run 'object'
DEBUG [2026-05-25 04:11:10] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:10] ========================================================
INFO [2026-05-25 04:11:10] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:10] ========================================================
INFO [2026-05-25 04:11:10] >> Contig Name: 'Achl_RBNII384-13'
INFO [2026-05-25 04:11:11] >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-25 04:11:11] >> Your contig name is Achl_RBNII384-13
SUCCESS [2026-05-25 04:11:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:11] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:11] >> 'Achl_RBNII384-13_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:11:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:11] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:11] >> 'Achl_RBNII384-13_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:11:11] >> The number of reads detected: 2
INFO [2026-05-25 04:11:11] Correcting frameshifts in reads using amino acidreference sequence
================================================================================
Time difference of 0.03 secs
SUCCESS [2026-05-25 04:11:12] ==========================================================
SUCCESS [2026-05-25 04:11:12] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:12] ==========================================================
INFO [2026-05-25 04:11:12] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:11:12] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:12] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-25 04:11:12] >> For more information, please run 'object'
DEBUG [2026-05-25 04:11:12] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:12] ------------------------------------------------
INFO [2026-05-25 04:11:12] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:12] ------------------------------------------------
INFO [2026-05-25 04:11:12] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:12] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:12] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:12] * Making basecall !!
INFO [2026-05-25 04:11:13] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:13] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:13] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:13] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:13] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:13] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:13] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:13] ------------------------------------------------
INFO [2026-05-25 04:11:13] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:13] ------------------------------------------------
INFO [2026-05-25 04:11:13] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:13] >> Creating Reverse Read raw abif ...
INFO [2026-05-25 04:11:13] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-25 04:11:13] * Making basecall !!
INFO [2026-05-25 04:11:13] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:13] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:13] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:13] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:13] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:13] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:13] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:13] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:13] ------------------------------------------------
INFO [2026-05-25 04:11:13] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:13] ------------------------------------------------
INFO [2026-05-25 04:11:13] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-25 04:11:14] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:14] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:14] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:14] ------------------------------------------------
INFO [2026-05-25 04:11:14] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:14] ------------------------------------------------
INFO [2026-05-25 04:11:14] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:11:14] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:14] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:14] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-25 04:11:14] FILE_NOT_EXIST_ERROR
'/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/TEST_Achl_ACHLO006-09_2_R.ab1' file does not exist.
DEBUG [2026-05-25 04:11:14] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:14] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:14] ------------------------------------------------
INFO [2026-05-25 04:11:14] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:14] ------------------------------------------------
INFO [2026-05-25 04:11:14] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:14] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:14] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:14] * Making basecall !!
INFO [2026-05-25 04:11:14] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:14] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:14] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:14] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:14] ========================================================
INFO [2026-05-25 04:11:14] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:14] ========================================================
INFO [2026-05-25 04:11:14] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:11:14] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:14] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:14] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:14] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:14] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:15] ==========================================================
SUCCESS [2026-05-25 04:11:15] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:15] ==========================================================
INFO [2026-05-25 04:11:15] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:15] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:15] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:15] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:15] >> For more information, please run 'object'
DEBUG [2026-05-25 04:11:15] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:15] #################################################
INFO [2026-05-25 04:11:15] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:15] #################################################
INFO [2026-05-25 04:11:15] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:15] ========================================================
INFO [2026-05-25 04:11:15] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:15] ========================================================
INFO [2026-05-25 04:11:15] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:15] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:15] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:15] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:15] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:15] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:15] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:15] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:15] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:15] ==========================================================
SUCCESS [2026-05-25 04:11:15] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:15] ==========================================================
INFO [2026-05-25 04:11:15] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:15] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:15] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:15] ========================================================
INFO [2026-05-25 04:11:15] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:15] ========================================================
INFO [2026-05-25 04:11:15] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:16] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:16] ==========================================================
SUCCESS [2026-05-25 04:11:16] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:16] ==========================================================
INFO [2026-05-25 04:11:16] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:16] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:16] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:16] ========================================================
INFO [2026-05-25 04:11:16] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:16] ========================================================
INFO [2026-05-25 04:11:16] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:16] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:16] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:16] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:17] ==========================================================
SUCCESS [2026-05-25 04:11:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:17] ==========================================================
INFO [2026-05-25 04:11:17] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:17] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:17] ========================================================
INFO [2026-05-25 04:11:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:17] ========================================================
INFO [2026-05-25 04:11:17] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:17] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:17] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:17] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:17] ==========================================================
SUCCESS [2026-05-25 04:11:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:17] ==========================================================
INFO [2026-05-25 04:11:17] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:17] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:17] Aligning consensus reads ...
INFO [2026-05-25 04:11:17] Before building!!
INFO [2026-05-25 04:11:17] After building!!
SUCCESS [2026-05-25 04:11:17] #############################################################
SUCCESS [2026-05-25 04:11:17] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:17] #############################################################
INFO [2026-05-25 04:11:17] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:17] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:17] >> 1 forward reads.
INFO [2026-05-25 04:11:17] >> 1 reverse reads.
INFO [2026-05-25 04:11:17] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:17] >> 1 forward reads.
INFO [2026-05-25 04:11:17] >> 1 reverse reads.
INFO [2026-05-25 04:11:17] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:17] >> 1 forward reads.
INFO [2026-05-25 04:11:17] >> 1 reverse reads.
INFO [2026-05-25 04:11:17] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:17] >> 1 forward reads.
INFO [2026-05-25 04:11:17] >> 1 reverse reads.
INFO [2026-05-25 04:11:17] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:17] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:17] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:17] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:18] * Making basecall !!
INFO [2026-05-25 04:11:18] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:11:18] ********************************************
INFO [2026-05-25 04:11:18] ******** SangerRead readTable print ********
INFO [2026-05-25 04:11:18] ********************************************
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Forward Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1
Read fileName (base) : Achl_ACHLO006-09_1_F.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 16
Trimming finish base pair : 477
Read length before trimming : 702
Read length after trimming : 461
Read quality before trimming : 52.87607
Read quality after trimming : 58.21041
Secondary peak cutoff : 0.33
Primary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
Secondary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
INFO [2026-05-25 04:11:18] **********************************************
INFO [2026-05-25 04:11:18] ******** SangerContig readTable print ********
INFO [2026-05-25 04:11:18] **********************************************
================================
=== SangerContig S4 instance ===
================================
Input source : ABIF
Names conversion CSV file :
Contig name : Achl_ACHLO006-09
Suffix forward regex : _[0-9]*_F.ab1$
Suffix reverse regex : _[0-9]*_R.ab1$
Minimum reads number : 2
Minimum read length : 20
Minimum fraction call : 0.5
Reference amino acid sequence : SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN
Maximum fraction lost : 0.5
Accept stop codons : TRUE
Reading frame : 1
Contig sequence : TTATATTTTATTCTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGGATTACGTCTTGAACGAATTCCCCTGTTTGTCTGAGCTGTGCTAATTACAGTTGTTCTTCTACTTCTATCTTTACCAGTGCTAGCAGGTGCCATTACCATACTTCTTACCGACCGAAACCTCAATACTTCATTCTTTGATCCTGCCGGTGGTGGAGACCCCATCCTC
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Forward Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1
Read fileName (base) : Achl_ACHLO006-09_1_F.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 16
Trimming finish base pair : 477
Read length before trimming : 702
Read length after trimming : 461
Read quality before trimming : 52.87607
Read quality after trimming : 58.21041
Secondary peak cutoff : 0.33
Primary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
Secondary Sequence : CTGGGCGTCTGAGCAGGAATGGTTGGAGCCGGTATAAGACTTCTAATTCGAATCGAGCTAAGACAACCAGGAGCGTTCCTGGGCAGAGACCAACTATACAATACTATCGTTACTGCACACGCATTTGTAATAATCTTCTTTCTAGTAATGCCTGTATTCATCGGGGGATTCGGAAACTGGCTTTTACCTTTAATACTTGGAGCCCCCGATATAGCATTCCCTCGACTCAACAACATGAGATTCTGACTACTTCCCCCATCACTGATCCTTTTAGTGTCCTCTGCGGCGGTAGAAAAAGGCGCTGGTACGGGGTGAACTGTTTATCCGCCTCTAGCAAGAAATCTTGCCCACGCAGGCCCGTCTGTAGATTTAGCCATCTTTTCCCTTCATTTAGCGGGTGCGTCTTCTATTCTAGGGGCTATTAATTTTATCACCACAGTTATTAATATGCGTTGAAGAGG
------------------------------
--- SangerRead S4 instance ---
------------------------------
Input source : ABIF
Read feature : Reverse Read
Read fileName (abs) : /Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata/Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_2_R.ab1
Read fileName (base) : Achl_ACHLO006-09_2_R.ab1
Trimming method : M1
Trimming cutoff : 1e-04
Trimming start base pair : 18
Trimming finish base pair : 658
Read length before trimming : 705
Read length after trimming : 640
Read quality before trimming : 54.85106
Read quality after trimming : 57.29531
Secondary peak cutoff : 0.33
Primary Sequence : GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGAGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA
Secondary Sequence : GAGGATGGGGTCTCCACCACCGGCAGGATCAAAGAATGAAGTATTGCGGTTTCGGTCGGTAAGAAGTATGGTAATGGCACCTGCTAGCACTGGTAAAGATAGAAGTAGAAGAACAACTGTAATTAGCACAGCTCAGACAAACAGGGGAATTCGTTCAAGACGTAATCCTCTTCAACGCATATTAATAACTGTGGTGATAAAATTAATAGCCCCTAGAATAGAAGACGCACCCGCTAAATGAAGGGAAAAGATGGCTAAATCTACAGACGGGCCTGCGTGGGCAAGATTTCTTGCTAGAGGCGGATAAACAGTTCACCCCGTACCAGCGCCTTTTTCTACCGCCGCAGAGGACACTAAAAGGATCAGTGATGGGGGAAGTAGTCAGAATCTCATGTTGTTGAGTCGAGGGAATGCTATATCGGGGGCTCCAAGTATTAAAGGTAAAAGCCAGTTTCCGAATCCCCCGATGAATACAGGCATTACTAGAAAGAAGATTATTACAAATGCGTGTGCAGTAACGATAGTATTGTATAGTTGGTCTCTGCCCAGGAACGCTCCTGGTTGTCTTAGCTCGATTCGAATTAGAAGTCTTATACCGGCTCCAACCATTCCTGCTCAGACGCCCAGAATAAAATATAAA
INFO [2026-05-25 04:11:19] Your input is 'SangerRead' S4 instance
INFO [2026-05-25 04:11:19] >>> outputDir : /tmp/RtmpC2hLks/file13c28e2e5fdeda
INFO [2026-05-25 04:11:19] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-25 04:11:19] >> '/tmp/RtmpC2hLks/file13c28e2e5fdeda/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-25 04:11:19] Your input is 'SangerContig' S4 instance
INFO [2026-05-25 04:11:19] >>> outputDir : /tmp/RtmpC2hLks/file13c28e2e5fdeda
INFO [2026-05-25 04:11:19] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-25 04:11:19] >> Writing alignment to FASTA ...
INFO [2026-05-25 04:11:19] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:11:19] >> Writing consensus read to FASTA ...
INFO [2026-05-25 04:11:19] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-25 04:11:19] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-25 04:11:19] >>> outputDir : /tmp/RtmpC2hLks/file13c28e2e5fdeda
INFO [2026-05-25 04:11:19] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-25 04:11:19] >> Writing 'alignment' to FASTA ...
INFO [2026-05-25 04:11:19] >> Writing 'contigs' to FASTA ...
INFO [2026-05-25 04:11:19] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:11:19] Finish writing 'SangerAlignment' to FASTA format
INFO [2026-05-25 04:11:19] #################################################
INFO [2026-05-25 04:11:19] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:19] #################################################
INFO [2026-05-25 04:11:19] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:19] ========================================================
INFO [2026-05-25 04:11:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:19] ========================================================
INFO [2026-05-25 04:11:19] >> Contig Name: 'Top'
SUCCESS [2026-05-25 04:11:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:19] >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:20] >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:20] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:20] ==========================================================
SUCCESS [2026-05-25 04:11:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:20] ==========================================================
INFO [2026-05-25 04:11:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:20] ========================================================
INFO [2026-05-25 04:11:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:20] ========================================================
INFO [2026-05-25 04:11:20] >> Contig Name: 'Nested'
SUCCESS [2026-05-25 04:11:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:20] >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:20] >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:20] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:20] ==========================================================
SUCCESS [2026-05-25 04:11:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:20] ==========================================================
INFO [2026-05-25 04:11:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:20] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:20] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:20] Aligning consensus reads ...
INFO [2026-05-25 04:11:20] Before building!!
INFO [2026-05-25 04:11:20] After building!!
INFO [2026-05-25 04:11:20] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-25 04:11:20] #############################################################
SUCCESS [2026-05-25 04:11:20] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:20] #############################################################
INFO [2026-05-25 04:11:20] >> 2 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:20] >> Contig 'Top':
INFO [2026-05-25 04:11:20] >> 1 forward reads.
INFO [2026-05-25 04:11:20] >> 1 reverse reads.
INFO [2026-05-25 04:11:20] >> Contig 'Nested':
INFO [2026-05-25 04:11:20] >> 1 forward reads.
INFO [2026-05-25 04:11:20] >> 1 reverse reads.
INFO [2026-05-25 04:11:20] >> 4 reads created from ABIF file.
INFO [2026-05-25 04:11:20] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:20] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:20] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:20] #################################################
INFO [2026-05-25 04:11:20] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:20] #################################################
INFO [2026-05-25 04:11:20] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:20] ========================================================
INFO [2026-05-25 04:11:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:20] ========================================================
INFO [2026-05-25 04:11:20] >> Contig Name: 'Top'
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] >> 'Top_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] >> 'Top_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:21] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:21] ==========================================================
SUCCESS [2026-05-25 04:11:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:21] ==========================================================
INFO [2026-05-25 04:11:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:21] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:21] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:21] ========================================================
INFO [2026-05-25 04:11:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:21] ========================================================
INFO [2026-05-25 04:11:21] >> Contig Name: 'Nested'
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] >> 'Nested_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:21] >> 'Nested_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:21] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:22] ==========================================================
SUCCESS [2026-05-25 04:11:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:22] ==========================================================
INFO [2026-05-25 04:11:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:22] Aligning consensus reads ...
INFO [2026-05-25 04:11:22] Before building!!
INFO [2026-05-25 04:11:22] After building!!
INFO [2026-05-25 04:11:22] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-25 04:11:22] #############################################################
SUCCESS [2026-05-25 04:11:22] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:22] #############################################################
INFO [2026-05-25 04:11:22] >> 2 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:22] >> Contig 'Top':
INFO [2026-05-25 04:11:22] >> 1 forward reads.
INFO [2026-05-25 04:11:22] >> 1 reverse reads.
INFO [2026-05-25 04:11:22] >> Contig 'Nested':
INFO [2026-05-25 04:11:22] >> 1 forward reads.
INFO [2026-05-25 04:11:22] >> 1 reverse reads.
INFO [2026-05-25 04:11:22] >> 4 reads created from ABIF file.
INFO [2026-05-25 04:11:22] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:22] #################################################
INFO [2026-05-25 04:11:22] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:22] #################################################
INFO [2026-05-25 04:11:22] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:22] ========================================================
INFO [2026-05-25 04:11:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:22] ========================================================
INFO [2026-05-25 04:11:22] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:22] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:22] ==========================================================
SUCCESS [2026-05-25 04:11:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:22] ==========================================================
INFO [2026-05-25 04:11:22] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:22] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:22] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:22] ========================================================
INFO [2026-05-25 04:11:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:22] ========================================================
INFO [2026-05-25 04:11:22] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:22] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:23] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:23] ==========================================================
SUCCESS [2026-05-25 04:11:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:23] ==========================================================
INFO [2026-05-25 04:11:23] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:23] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:23] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:23] ========================================================
INFO [2026-05-25 04:11:23] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:23] ========================================================
INFO [2026-05-25 04:11:23] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:23] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:23] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:23] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:23] ==========================================================
SUCCESS [2026-05-25 04:11:23] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:23] ==========================================================
INFO [2026-05-25 04:11:23] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:23] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:24] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:24] ========================================================
INFO [2026-05-25 04:11:24] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:24] ========================================================
INFO [2026-05-25 04:11:24] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:24] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:24] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:24] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:24] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:24] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:24] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:24] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:24] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:24] ==========================================================
SUCCESS [2026-05-25 04:11:24] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:24] ==========================================================
INFO [2026-05-25 04:11:24] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:24] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:24] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:24] Aligning consensus reads ...
INFO [2026-05-25 04:11:24] Before building!!
INFO [2026-05-25 04:11:24] After building!!
SUCCESS [2026-05-25 04:11:24] #############################################################
SUCCESS [2026-05-25 04:11:24] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:24] #############################################################
INFO [2026-05-25 04:11:24] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:24] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:24] >> 1 forward reads.
INFO [2026-05-25 04:11:24] >> 1 reverse reads.
INFO [2026-05-25 04:11:24] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:24] >> 1 forward reads.
INFO [2026-05-25 04:11:24] >> 1 reverse reads.
INFO [2026-05-25 04:11:24] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:24] >> 1 forward reads.
INFO [2026-05-25 04:11:24] >> 1 reverse reads.
INFO [2026-05-25 04:11:24] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:24] >> 1 forward reads.
INFO [2026-05-25 04:11:24] >> 1 reverse reads.
INFO [2026-05-25 04:11:24] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:24] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:24] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:24] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:25] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:25] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:25] * Making basecall !!
INFO [2026-05-25 04:11:25] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:25] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:25] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:25] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:25] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:25] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:25] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:25] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:25] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:25] * Making basecall !!
INFO [2026-05-25 04:11:25] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:25] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:25] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:25] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:25] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:25] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:25] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:25] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:25] ------------------------------------------------
INFO [2026-05-25 04:11:25] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:25] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:26] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:26] * Making basecall !!
INFO [2026-05-25 04:11:26] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:26] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:26] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:26] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:26] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:26] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:26] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:26] ------------------------------------------------
INFO [2026-05-25 04:11:26] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:26] ------------------------------------------------
INFO [2026-05-25 04:11:26] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:26] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:26] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:26] * Making basecall !!
INFO [2026-05-25 04:11:26] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:26] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:26] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:26] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:26] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:26] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:26] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:26] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:27] ------------------------------------------------
INFO [2026-05-25 04:11:27] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:27] ------------------------------------------------
INFO [2026-05-25 04:11:27] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:27] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:27] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:27] * Making basecall !!
INFO [2026-05-25 04:11:27] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:27] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:27] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:27] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:27] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:27] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:27] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:27] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:28] #################################################
INFO [2026-05-25 04:11:28] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:28] #################################################
INFO [2026-05-25 04:11:28] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:28] ========================================================
INFO [2026-05-25 04:11:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:28] ========================================================
INFO [2026-05-25 04:11:28] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:28] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:28] ==========================================================
SUCCESS [2026-05-25 04:11:28] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:28] ==========================================================
INFO [2026-05-25 04:11:28] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:28] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:28] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:28] ========================================================
INFO [2026-05-25 04:11:28] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:28] ========================================================
INFO [2026-05-25 04:11:28] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:28] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:28] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:28] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:29] ==========================================================
SUCCESS [2026-05-25 04:11:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:29] ==========================================================
INFO [2026-05-25 04:11:29] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:29] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:29] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:29] ========================================================
INFO [2026-05-25 04:11:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:29] ========================================================
INFO [2026-05-25 04:11:29] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:29] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:29] ==========================================================
SUCCESS [2026-05-25 04:11:29] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:29] ==========================================================
INFO [2026-05-25 04:11:29] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:29] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:29] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:29] ========================================================
INFO [2026-05-25 04:11:29] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:29] ========================================================
INFO [2026-05-25 04:11:29] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:29] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:29] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:30] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:30] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:30] ==========================================================
SUCCESS [2026-05-25 04:11:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:30] ==========================================================
INFO [2026-05-25 04:11:30] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:30] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:30] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:30] Aligning consensus reads ...
INFO [2026-05-25 04:11:30] Before building!!
INFO [2026-05-25 04:11:30] After building!!
SUCCESS [2026-05-25 04:11:30] #############################################################
SUCCESS [2026-05-25 04:11:30] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:30] #############################################################
INFO [2026-05-25 04:11:30] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:30] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:30] >> 1 forward reads.
INFO [2026-05-25 04:11:30] >> 1 reverse reads.
INFO [2026-05-25 04:11:30] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:30] >> 1 forward reads.
INFO [2026-05-25 04:11:30] >> 1 reverse reads.
INFO [2026-05-25 04:11:30] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:30] >> 1 forward reads.
INFO [2026-05-25 04:11:30] >> 1 reverse reads.
INFO [2026-05-25 04:11:30] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:30] >> 1 forward reads.
INFO [2026-05-25 04:11:30] >> 1 reverse reads.
INFO [2026-05-25 04:11:30] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:30] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:30] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:30] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:30] #################################################
INFO [2026-05-25 04:11:30] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:30] #################################################
INFO [2026-05-25 04:11:30] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:30] ========================================================
INFO [2026-05-25 04:11:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:30] ========================================================
INFO [2026-05-25 04:11:30] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:11:31] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:31] ==========================================================
SUCCESS [2026-05-25 04:11:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:31] ==========================================================
INFO [2026-05-25 04:11:31] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:31] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:31] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:31] ========================================================
INFO [2026-05-25 04:11:31] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:31] ========================================================
INFO [2026-05-25 04:11:31] >> Contig Name: 'Achl_ACHLO007-09'
INFO [2026-05-25 04:11:32] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:32] ==========================================================
SUCCESS [2026-05-25 04:11:32] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:32] ==========================================================
INFO [2026-05-25 04:11:32] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:32] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:32] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:32] ========================================================
INFO [2026-05-25 04:11:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:32] ========================================================
INFO [2026-05-25 04:11:32] >> Contig Name: 'Achl_ACHLO040-09'
INFO [2026-05-25 04:11:33] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:33] ==========================================================
SUCCESS [2026-05-25 04:11:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:33] ==========================================================
INFO [2026-05-25 04:11:33] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:33] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:33] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:33] ========================================================
INFO [2026-05-25 04:11:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:33] ========================================================
INFO [2026-05-25 04:11:33] >> Contig Name: 'Achl_ACHLO041-09'
INFO [2026-05-25 04:11:34] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:34] ==========================================================
SUCCESS [2026-05-25 04:11:34] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:34] ==========================================================
INFO [2026-05-25 04:11:34] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:34] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:34] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:34] Aligning consensus reads ...
INFO [2026-05-25 04:11:34] Before building!!
INFO [2026-05-25 04:11:34] After building!!
SUCCESS [2026-05-25 04:11:34] #############################################################
SUCCESS [2026-05-25 04:11:34] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:34] #############################################################
INFO [2026-05-25 04:11:34] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:34] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:34] >> 1 forward reads.
INFO [2026-05-25 04:11:34] >> 1 reverse reads.
INFO [2026-05-25 04:11:34] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:34] >> 1 forward reads.
INFO [2026-05-25 04:11:34] >> 1 reverse reads.
INFO [2026-05-25 04:11:34] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:34] >> 1 forward reads.
INFO [2026-05-25 04:11:34] >> 1 reverse reads.
INFO [2026-05-25 04:11:34] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:34] >> 1 forward reads.
INFO [2026-05-25 04:11:34] >> 1 reverse reads.
INFO [2026-05-25 04:11:34] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:34] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:34] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:34] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:34] #################################################
INFO [2026-05-25 04:11:34] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:34] #################################################
INFO [2026-05-25 04:11:34] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:34] ========================================================
INFO [2026-05-25 04:11:34] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:34] ========================================================
INFO [2026-05-25 04:11:34] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:34] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:35] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:35] ==========================================================
SUCCESS [2026-05-25 04:11:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:35] ==========================================================
INFO [2026-05-25 04:11:35] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:35] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:35] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:35] ========================================================
INFO [2026-05-25 04:11:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:35] ========================================================
INFO [2026-05-25 04:11:35] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:35] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:35] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:36] ==========================================================
SUCCESS [2026-05-25 04:11:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:36] ==========================================================
INFO [2026-05-25 04:11:36] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:36] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:36] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:36] ========================================================
INFO [2026-05-25 04:11:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:36] ========================================================
INFO [2026-05-25 04:11:36] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:36] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:36] ==========================================================
SUCCESS [2026-05-25 04:11:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:36] ==========================================================
INFO [2026-05-25 04:11:36] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:36] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:36] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:36] ========================================================
INFO [2026-05-25 04:11:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:36] ========================================================
INFO [2026-05-25 04:11:36] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:36] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:36] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:37] ==========================================================
SUCCESS [2026-05-25 04:11:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:37] ==========================================================
INFO [2026-05-25 04:11:37] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:37] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:37] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:37] Aligning consensus reads ...
INFO [2026-05-25 04:11:37] Before building!!
INFO [2026-05-25 04:11:37] After building!!
SUCCESS [2026-05-25 04:11:37] #############################################################
SUCCESS [2026-05-25 04:11:37] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:37] #############################################################
INFO [2026-05-25 04:11:37] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:37] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:37] >> 1 forward reads.
INFO [2026-05-25 04:11:37] >> 1 reverse reads.
INFO [2026-05-25 04:11:37] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:37] >> 1 forward reads.
INFO [2026-05-25 04:11:37] >> 1 reverse reads.
INFO [2026-05-25 04:11:37] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:37] >> 1 forward reads.
INFO [2026-05-25 04:11:37] >> 1 reverse reads.
INFO [2026-05-25 04:11:37] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:37] >> 1 forward reads.
INFO [2026-05-25 04:11:37] >> 1 reverse reads.
INFO [2026-05-25 04:11:37] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:37] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:37] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:37] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:37] ------------------------------------------------
INFO [2026-05-25 04:11:37] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:37] ------------------------------------------------
INFO [2026-05-25 04:11:37] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:37] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:37] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:37] * Making basecall !!
INFO [2026-05-25 04:11:37] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:37] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:37] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:37] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:37] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:37] ------------------------------------------------
INFO [2026-05-25 04:11:37] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:37] ------------------------------------------------
INFO [2026-05-25 04:11:37] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:37] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:37] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:37] * Making basecall !!
INFO [2026-05-25 04:11:37] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:37] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:37] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:37] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:37] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:38] ------------------------------------------------
INFO [2026-05-25 04:11:38] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:38] ------------------------------------------------
INFO [2026-05-25 04:11:38] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:38] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:38] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:38] * Making basecall !!
INFO [2026-05-25 04:11:38] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:38] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:38] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:38] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:38] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:38] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:38] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:38] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:39] ------------------------------------------------
INFO [2026-05-25 04:11:39] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:11:39] ------------------------------------------------
INFO [2026-05-25 04:11:39] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:11:39] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:11:39] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:11:39] * Making basecall !!
INFO [2026-05-25 04:11:39] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:11:39] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:39] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:39] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:39] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:11:39] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:39] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:39] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:11:40] #################################################
INFO [2026-05-25 04:11:40] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:40] #################################################
INFO [2026-05-25 04:11:40] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:40] ========================================================
INFO [2026-05-25 04:11:40] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:40] ========================================================
INFO [2026-05-25 04:11:40] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:40] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:40] ==========================================================
SUCCESS [2026-05-25 04:11:40] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:40] ==========================================================
INFO [2026-05-25 04:11:40] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:40] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:40] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:40] ========================================================
INFO [2026-05-25 04:11:40] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:40] ========================================================
INFO [2026-05-25 04:11:40] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:40] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:40] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:41] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:41] ==========================================================
SUCCESS [2026-05-25 04:11:41] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:41] ==========================================================
INFO [2026-05-25 04:11:41] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:41] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:41] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:41] ========================================================
INFO [2026-05-25 04:11:41] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:41] ========================================================
INFO [2026-05-25 04:11:41] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:41] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:41] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:41] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:41] ==========================================================
SUCCESS [2026-05-25 04:11:41] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:41] ==========================================================
INFO [2026-05-25 04:11:41] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:41] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:41] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:41] ========================================================
INFO [2026-05-25 04:11:41] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:41] ========================================================
INFO [2026-05-25 04:11:41] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:42] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:42] ==========================================================
SUCCESS [2026-05-25 04:11:42] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:42] ==========================================================
INFO [2026-05-25 04:11:42] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:42] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:42] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:42] Aligning consensus reads ...
INFO [2026-05-25 04:11:42] Before building!!
INFO [2026-05-25 04:11:42] After building!!
SUCCESS [2026-05-25 04:11:42] #############################################################
SUCCESS [2026-05-25 04:11:42] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:42] #############################################################
INFO [2026-05-25 04:11:42] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:42] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:42] >> 1 forward reads.
INFO [2026-05-25 04:11:42] >> 1 reverse reads.
INFO [2026-05-25 04:11:42] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:42] >> 1 forward reads.
INFO [2026-05-25 04:11:42] >> 1 reverse reads.
INFO [2026-05-25 04:11:42] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:42] >> 1 forward reads.
INFO [2026-05-25 04:11:42] >> 1 reverse reads.
INFO [2026-05-25 04:11:42] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:42] >> 1 forward reads.
INFO [2026-05-25 04:11:42] >> 1 reverse reads.
INFO [2026-05-25 04:11:42] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:42] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:42] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:42] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:42] #################################################
INFO [2026-05-25 04:11:42] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:42] #################################################
INFO [2026-05-25 04:11:42] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:11:42] ========================================================
INFO [2026-05-25 04:11:42] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:42] ========================================================
INFO [2026-05-25 04:11:42] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:42] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:42] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:43] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:43] ==========================================================
SUCCESS [2026-05-25 04:11:43] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:43] ==========================================================
INFO [2026-05-25 04:11:43] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:43] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:43] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:43] ========================================================
INFO [2026-05-25 04:11:43] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:43] ========================================================
INFO [2026-05-25 04:11:43] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:43] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:43] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:43] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:44] ==========================================================
SUCCESS [2026-05-25 04:11:44] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:44] ==========================================================
INFO [2026-05-25 04:11:44] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:44] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:44] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:44] ========================================================
INFO [2026-05-25 04:11:44] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:44] ========================================================
INFO [2026-05-25 04:11:44] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:44] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:44] ==========================================================
SUCCESS [2026-05-25 04:11:44] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:44] ==========================================================
INFO [2026-05-25 04:11:44] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:44] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:44] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:44] ========================================================
INFO [2026-05-25 04:11:44] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:44] ========================================================
INFO [2026-05-25 04:11:44] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:44] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:44] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:45] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:45] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:45] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:45] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:45] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:45] ==========================================================
SUCCESS [2026-05-25 04:11:45] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:45] ==========================================================
INFO [2026-05-25 04:11:45] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:45] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:11:45] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:11:45] Aligning consensus reads ...
INFO [2026-05-25 04:11:45] Before building!!
INFO [2026-05-25 04:11:45] After building!!
SUCCESS [2026-05-25 04:11:45] #############################################################
SUCCESS [2026-05-25 04:11:45] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:45] #############################################################
INFO [2026-05-25 04:11:45] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:11:45] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:45] >> 1 forward reads.
INFO [2026-05-25 04:11:45] >> 1 reverse reads.
INFO [2026-05-25 04:11:45] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:45] >> 1 forward reads.
INFO [2026-05-25 04:11:45] >> 1 reverse reads.
INFO [2026-05-25 04:11:45] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:45] >> 1 forward reads.
INFO [2026-05-25 04:11:45] >> 1 reverse reads.
INFO [2026-05-25 04:11:45] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:45] >> 1 forward reads.
INFO [2026-05-25 04:11:45] >> 1 reverse reads.
INFO [2026-05-25 04:11:45] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:45] >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-25 04:11:45] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:45] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:45] #################################################
INFO [2026-05-25 04:11:45] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:45] #################################################
INFO [2026-05-25 04:11:45] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-25 04:11:45] **** Contig number in your Csv file is 4
INFO [2026-05-25 04:11:45] ========================================================
INFO [2026-05-25 04:11:45] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:45] ========================================================
INFO [2026-05-25 04:11:45] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:45] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:45] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:45] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:45] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:46] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:46] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:46] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:47] ==========================================================
SUCCESS [2026-05-25 04:11:47] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:47] ==========================================================
INFO [2026-05-25 04:11:47] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:47] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:47] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:47] ========================================================
INFO [2026-05-25 04:11:47] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:47] ========================================================
INFO [2026-05-25 04:11:47] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:47] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:48] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:48] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:49] ==========================================================
SUCCESS [2026-05-25 04:11:49] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:49] ==========================================================
INFO [2026-05-25 04:11:49] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:49] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:49] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:49] ========================================================
INFO [2026-05-25 04:11:49] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:49] ========================================================
INFO [2026-05-25 04:11:49] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:50] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:50] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:50] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:51] ==========================================================
SUCCESS [2026-05-25 04:11:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:51] ==========================================================
INFO [2026-05-25 04:11:51] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:51] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:51] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:51] ========================================================
INFO [2026-05-25 04:11:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:51] ========================================================
INFO [2026-05-25 04:11:51] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:51] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:51] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:51] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:52] ==========================================================
SUCCESS [2026-05-25 04:11:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:52] ==========================================================
INFO [2026-05-25 04:11:52] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:52] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:52] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:52] Aligning consensus reads ...
INFO [2026-05-25 04:11:52] Before building!!
INFO [2026-05-25 04:11:52] After building!!
SUCCESS [2026-05-25 04:11:52] #############################################################
SUCCESS [2026-05-25 04:11:52] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:11:52] #############################################################
INFO [2026-05-25 04:11:52] >> 4 contigs detected from 'csv file'.
INFO [2026-05-25 04:11:52] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:11:52] >> 1 forward reads.
INFO [2026-05-25 04:11:52] >> 1 reverse reads.
INFO [2026-05-25 04:11:52] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:11:52] >> 1 forward reads.
INFO [2026-05-25 04:11:52] >> 1 reverse reads.
INFO [2026-05-25 04:11:52] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:11:52] >> 1 forward reads.
INFO [2026-05-25 04:11:52] >> 1 reverse reads.
INFO [2026-05-25 04:11:52] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:11:52] >> 1 forward reads.
INFO [2026-05-25 04:11:53] >> 1 reverse reads.
INFO [2026-05-25 04:11:53] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:11:53] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:11:53] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:11:53] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:11:53] #################################################
INFO [2026-05-25 04:11:53] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:11:53] #################################################
INFO [2026-05-25 04:11:53] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-25 04:11:53] **** Contig number in your Csv file is 4
INFO [2026-05-25 04:11:53] ========================================================
INFO [2026-05-25 04:11:53] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:53] ========================================================
INFO [2026-05-25 04:11:53] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:11:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:53] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:54] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:54] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:55] ==========================================================
SUCCESS [2026-05-25 04:11:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:55] ==========================================================
INFO [2026-05-25 04:11:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:55] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:55] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:55] ========================================================
INFO [2026-05-25 04:11:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:55] ========================================================
INFO [2026-05-25 04:11:55] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:11:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:55] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:56] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:56] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:57] ==========================================================
SUCCESS [2026-05-25 04:11:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:57] ==========================================================
INFO [2026-05-25 04:11:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:57] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:57] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:57] ========================================================
INFO [2026-05-25 04:11:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:57] ========================================================
INFO [2026-05-25 04:11:57] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:11:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:57] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:58] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:58] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:11:59] ==========================================================
SUCCESS [2026-05-25 04:11:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:11:59] ==========================================================
INFO [2026-05-25 04:11:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:11:59] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:11:59] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:11:59] ========================================================
INFO [2026-05-25 04:11:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:11:59] ========================================================
INFO [2026-05-25 04:11:59] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:11:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:59] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:11:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:11:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:11:59] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:11:59] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:00] ==========================================================
SUCCESS [2026-05-25 04:12:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:00] ==========================================================
INFO [2026-05-25 04:12:00] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:00] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:00] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:00] Aligning consensus reads ...
INFO [2026-05-25 04:12:00] Before building!!
INFO [2026-05-25 04:12:00] After building!!
SUCCESS [2026-05-25 04:12:00] #############################################################
SUCCESS [2026-05-25 04:12:00] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:00] #############################################################
INFO [2026-05-25 04:12:00] >> 4 contigs detected from 'csv file'.
INFO [2026-05-25 04:12:00] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:00] >> 1 forward reads.
INFO [2026-05-25 04:12:00] >> 1 reverse reads.
INFO [2026-05-25 04:12:00] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:00] >> 1 forward reads.
INFO [2026-05-25 04:12:00] >> 1 reverse reads.
INFO [2026-05-25 04:12:00] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:00] >> 1 forward reads.
INFO [2026-05-25 04:12:00] >> 1 reverse reads.
INFO [2026-05-25 04:12:00] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:00] >> 1 forward reads.
INFO [2026-05-25 04:12:00] >> 1 reverse reads.
INFO [2026-05-25 04:12:00] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:12:00] >> Reads are trimmed by 'M2 - sliding window method'.
DEBUG [2026-05-25 04:12:00] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:00] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:00] #################################################
INFO [2026-05-25 04:12:00] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:00] #################################################
INFO [2026-05-25 04:12:00] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:12:00] ========================================================
INFO [2026-05-25 04:12:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:00] ========================================================
INFO [2026-05-25 04:12:00] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:00] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:00] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:00] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:01] ==========================================================
SUCCESS [2026-05-25 04:12:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:01] ==========================================================
INFO [2026-05-25 04:12:01] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:01] ========================================================
INFO [2026-05-25 04:12:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:01] ========================================================
INFO [2026-05-25 04:12:01] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:01] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:01] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:01] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:02] ==========================================================
SUCCESS [2026-05-25 04:12:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:02] ==========================================================
INFO [2026-05-25 04:12:02] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:02] ========================================================
INFO [2026-05-25 04:12:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:02] ========================================================
INFO [2026-05-25 04:12:02] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:04] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:04] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:04] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:05] ==========================================================
SUCCESS [2026-05-25 04:12:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:05] ==========================================================
INFO [2026-05-25 04:12:05] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:05] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:05] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:05] ========================================================
INFO [2026-05-25 04:12:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:05] ========================================================
INFO [2026-05-25 04:12:05] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:05] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:05] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:05] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:05] ==========================================================
SUCCESS [2026-05-25 04:12:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:05] ==========================================================
INFO [2026-05-25 04:12:05] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:05] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:05] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:05] Aligning consensus reads ...
INFO [2026-05-25 04:12:05] Before building!!
INFO [2026-05-25 04:12:05] After building!!
SUCCESS [2026-05-25 04:12:05] #############################################################
SUCCESS [2026-05-25 04:12:05] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:05] #############################################################
INFO [2026-05-25 04:12:05] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:12:06] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:06] >> 1 forward reads.
INFO [2026-05-25 04:12:06] >> 1 reverse reads.
INFO [2026-05-25 04:12:06] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:06] >> 1 forward reads.
INFO [2026-05-25 04:12:06] >> 1 reverse reads.
INFO [2026-05-25 04:12:06] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:06] >> 1 forward reads.
INFO [2026-05-25 04:12:06] >> 1 reverse reads.
INFO [2026-05-25 04:12:06] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:06] >> 1 forward reads.
INFO [2026-05-25 04:12:06] >> 1 reverse reads.
INFO [2026-05-25 04:12:06] >> 8 reads created from FASTA file.
DEBUG [2026-05-25 04:12:06] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:06] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:06] #################################################
INFO [2026-05-25 04:12:06] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:06] #################################################
INFO [2026-05-25 04:12:06] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-25 04:12:06] ========================================================
INFO [2026-05-25 04:12:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:06] ========================================================
INFO [2026-05-25 04:12:06] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:06] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:06] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:06] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:07] ==========================================================
SUCCESS [2026-05-25 04:12:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:07] ==========================================================
INFO [2026-05-25 04:12:07] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:07] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:07] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:07] ========================================================
INFO [2026-05-25 04:12:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:07] ========================================================
INFO [2026-05-25 04:12:07] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:07] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:07] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:07] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:07] ==========================================================
SUCCESS [2026-05-25 04:12:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:07] ==========================================================
INFO [2026-05-25 04:12:07] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:07] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:07] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:07] ========================================================
INFO [2026-05-25 04:12:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:07] ========================================================
INFO [2026-05-25 04:12:08] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:08] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:08] ==========================================================
SUCCESS [2026-05-25 04:12:08] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:08] ==========================================================
INFO [2026-05-25 04:12:08] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:08] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:08] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:08] ========================================================
INFO [2026-05-25 04:12:08] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:08] ========================================================
INFO [2026-05-25 04:12:08] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:08] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:08] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:09] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:09] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:09] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:09] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:09] ==========================================================
SUCCESS [2026-05-25 04:12:09] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:09] ==========================================================
INFO [2026-05-25 04:12:09] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:09] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:09] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:09] Aligning consensus reads ...
INFO [2026-05-25 04:12:09] Before building!!
INFO [2026-05-25 04:12:09] After building!!
SUCCESS [2026-05-25 04:12:09] #############################################################
SUCCESS [2026-05-25 04:12:09] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:09] #############################################################
INFO [2026-05-25 04:12:09] >> 4 contigs detected from 'csv file'.
INFO [2026-05-25 04:12:09] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:09] >> 1 forward reads.
INFO [2026-05-25 04:12:09] >> 1 reverse reads.
INFO [2026-05-25 04:12:09] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:09] >> 1 forward reads.
INFO [2026-05-25 04:12:09] >> 1 reverse reads.
INFO [2026-05-25 04:12:09] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:09] >> 1 forward reads.
INFO [2026-05-25 04:12:09] >> 1 reverse reads.
INFO [2026-05-25 04:12:09] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:09] >> 1 forward reads.
INFO [2026-05-25 04:12:09] >> 1 reverse reads.
INFO [2026-05-25 04:12:09] >> 8 reads created from FASTA file.
DEBUG [2026-05-25 04:12:09] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:09] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
SUCCESS [2026-05-25 04:12:10] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
SUCCESS [2026-05-25 04:12:10] 'Achl_ACHLO006-09' is successfully created!
SUCCESS [2026-05-25 04:12:10] 'SangerAlignment' is successfully created!
ERROR [2026-05-25 04:12:10] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
DEBUG [2026-05-25 04:12:10] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:10] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-25 04:12:10] FILE_NOT_EXIST_ERROR
'/no/such/path.ab1' file does not exist.
INFO [2026-05-25 04:12:10] ------------------------------------------------
INFO [2026-05-25 04:12:10] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:10] ------------------------------------------------
INFO [2026-05-25 04:12:10] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:12:10] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:12:10] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:12:10] * Making basecall !!
INFO [2026-05-25 04:12:10] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:12:10] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:10] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:10] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:11] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:11] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:11] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:11] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-25 04:12:11] 'Achl_ACHLO006-09_1_F.ab1' is successfully created!
INFO [2026-05-25 04:12:11] ------------------------------------------------
INFO [2026-05-25 04:12:11] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:11] ------------------------------------------------
INFO [2026-05-25 04:12:11] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-25 04:12:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:11] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:11] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:11] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-25 04:12:11] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:11] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:11] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
SUCCESS [2026-05-25 04:12:11] 'Achl_ACHLO006-09_1_F.fa' is successfully created!
ERROR [2026-05-25 04:12:11] 'object' must be S4 instance!
ERROR [2026-05-25 04:12:11] 'object' must be 'SangerAlignment' or 'SangerContig' S4 instance!
INFO [2026-05-25 04:12:11] Your input is 'SangerRead' S4 instance
INFO [2026-05-25 04:12:11] >>> outputDir : /tmp/RtmpC2hLks/file13c28e499d799a
INFO [2026-05-25 04:12:11] Start writing '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-25 04:12:11] >> '/tmp/RtmpC2hLks/file13c28e499d799a/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-25 04:12:11] Your input is 'SangerContig' S4 instance
INFO [2026-05-25 04:12:11] >>> outputDir : /tmp/RtmpC2hLks/file13c28e499d799a
INFO [2026-05-25 04:12:11] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-25 04:12:11] >> Writing alignment to FASTA ...
INFO [2026-05-25 04:12:11] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:12:11] >> Writing consensus read to FASTA ...
INFO [2026-05-25 04:12:11] Finish writing 'Achl_ACHLO006-09' to FASTA format
INFO [2026-05-25 04:12:11] Your input is 'SangerAlignment' S4 instance
INFO [2026-05-25 04:12:11] >>> outputDir : /tmp/RtmpC2hLks/file13c28e499d799a
INFO [2026-05-25 04:12:11] Start to write 'SangerAlignment' to FASTA format ...
INFO [2026-05-25 04:12:11] >> Writing 'alignment' to FASTA ...
INFO [2026-05-25 04:12:11] >> Writing 'contigs' to FASTA ...
INFO [2026-05-25 04:12:11] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:12:11] Finish writing 'SangerAlignment' to FASTA format
ERROR [2026-05-25 04:12:11] 'object' must be S4 instance!
ERROR [2026-05-25 04:12:11] 'object' must be S4 instance!
INFO [2026-05-25 04:12:16] * Making basecall !!
INFO [2026-05-25 04:12:16] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:12:17] #################################################
INFO [2026-05-25 04:12:17] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:17] #################################################
INFO [2026-05-25 04:12:17] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:17] ========================================================
INFO [2026-05-25 04:12:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:17] ========================================================
INFO [2026-05-25 04:12:17] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:17] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:17] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:17] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:17] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:17] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:17] ==========================================================
SUCCESS [2026-05-25 04:12:17] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:17] ==========================================================
INFO [2026-05-25 04:12:17] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:17] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:17] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:17] ========================================================
INFO [2026-05-25 04:12:17] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:17] ========================================================
INFO [2026-05-25 04:12:17] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:18] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:18] ==========================================================
SUCCESS [2026-05-25 04:12:18] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:18] ==========================================================
INFO [2026-05-25 04:12:18] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:18] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:18] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:18] ========================================================
INFO [2026-05-25 04:12:18] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:18] ========================================================
INFO [2026-05-25 04:12:18] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:18] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:18] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:19] ==========================================================
SUCCESS [2026-05-25 04:12:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:19] ==========================================================
INFO [2026-05-25 04:12:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:19] ========================================================
INFO [2026-05-25 04:12:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:19] ========================================================
INFO [2026-05-25 04:12:19] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:19] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:19] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:19] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:19] ==========================================================
SUCCESS [2026-05-25 04:12:19] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:19] ==========================================================
INFO [2026-05-25 04:12:19] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:19] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:19] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:19] Aligning consensus reads ...
INFO [2026-05-25 04:12:19] Before building!!
INFO [2026-05-25 04:12:19] After building!!
SUCCESS [2026-05-25 04:12:19] #############################################################
SUCCESS [2026-05-25 04:12:19] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:19] #############################################################
INFO [2026-05-25 04:12:19] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:12:19] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:19] >> 1 forward reads.
INFO [2026-05-25 04:12:19] >> 1 reverse reads.
INFO [2026-05-25 04:12:19] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:19] >> 1 forward reads.
INFO [2026-05-25 04:12:19] >> 1 reverse reads.
INFO [2026-05-25 04:12:19] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:19] >> 1 forward reads.
INFO [2026-05-25 04:12:19] >> 1 reverse reads.
INFO [2026-05-25 04:12:19] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:19] >> 1 forward reads.
INFO [2026-05-25 04:12:19] >> 1 reverse reads.
INFO [2026-05-25 04:12:19] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:12:19] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:24] Aligning consensus reads ...
INFO [2026-05-25 04:12:24] Before building!!
INFO [2026-05-25 04:12:24] After building!!
INFO [2026-05-25 04:12:29] Aligning consensus reads ...
INFO [2026-05-25 04:12:29] Before building!!
INFO [2026-05-25 04:12:29] After building!!
INFO [2026-05-25 04:12:30] #################################################
INFO [2026-05-25 04:12:30] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:30] #################################################
INFO [2026-05-25 04:12:30] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:30] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:30] ==========================================================
SUCCESS [2026-05-25 04:12:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:30] ==========================================================
INFO [2026-05-25 04:12:30] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:30] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:30] ==========================================================
SUCCESS [2026-05-25 04:12:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:30] ==========================================================
INFO [2026-05-25 04:12:30] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:30] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:30] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:30] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:30] ==========================================================
SUCCESS [2026-05-25 04:12:30] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:30] ==========================================================
INFO [2026-05-25 04:12:30] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:30] ========================================================
INFO [2026-05-25 04:12:30] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:31] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:31] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:31] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:31] ==========================================================
SUCCESS [2026-05-25 04:12:31] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:31] ==========================================================
INFO [2026-05-25 04:12:31] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:31] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:31] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:31] Aligning consensus reads ...
INFO [2026-05-25 04:12:31] Before building!!
INFO [2026-05-25 04:12:31] After building!!
SUCCESS [2026-05-25 04:12:31] #############################################################
SUCCESS [2026-05-25 04:12:31] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:31] #############################################################
INFO [2026-05-25 04:12:31] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:12:31] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:31] >> 1 forward reads.
INFO [2026-05-25 04:12:31] >> 1 reverse reads.
INFO [2026-05-25 04:12:31] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:31] >> 1 forward reads.
INFO [2026-05-25 04:12:31] >> 1 reverse reads.
INFO [2026-05-25 04:12:31] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:31] >> 1 forward reads.
INFO [2026-05-25 04:12:31] >> 1 reverse reads.
INFO [2026-05-25 04:12:31] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:31] >> 1 forward reads.
INFO [2026-05-25 04:12:31] >> 1 reverse reads.
INFO [2026-05-25 04:12:31] >> 8 reads created from FASTA file.
DEBUG [2026-05-25 04:12:31] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:31] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:31] SangerAlignment with 'FASTA' inputSource cannot update quality parameters
ERROR [2026-05-25 04:12:31] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
ERROR [2026-05-25 04:12:31] PARAMETER_VALUE_ERROR'TrimmingMethod' must be 'M1' or 'M2'.
INFO [2026-05-25 04:12:31] >>> outputDir : /tmp/RtmpC2hLks/file13c28e62d20595
INFO [2026-05-25 04:12:32] * Making basecall !!
INFO [2026-05-25 04:12:32] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:12:33] Chromatogram saved to /tmp/RtmpC2hLks/file13c28e62d20595/Achl_ACHLO006-09_1_F/Chromatogram.pdf in the current working directory
/usr/bin/pandoc +RTS -K512m -RTS SangerRead_Report_ab1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpC2hLks/file13c28e62d20595/Achl_ACHLO006-09_1_F/SangerRead_Report_ab1.html --lua-filter /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /home/biocbuild/bbs-3.24-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpC2hLks/rmarkdown-str13c28e51cbb0d.html
INFO [2026-05-25 04:12:46] ------------------------------------------------
INFO [2026-05-25 04:12:46] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:46] ------------------------------------------------
INFO [2026-05-25 04:12:46] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:12:46] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:12:46] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:12:46] * Making basecall !!
INFO [2026-05-25 04:12:46] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:12:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:46] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:46] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:46] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:46] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:46] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:46] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:12:46] ------------------------------------------------
INFO [2026-05-25 04:12:46] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:46] ------------------------------------------------
INFO [2026-05-25 04:12:46] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:12:46] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:12:47] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:12:47] * Making basecall !!
INFO [2026-05-25 04:12:47] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:47] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:47] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:47] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:47] >> You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:12:47] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:47] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:47] ==========================================================
SUCCESS [2026-05-25 04:12:47] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:47] ==========================================================
INFO [2026-05-25 04:12:47] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:47] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:47] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
DEBUG [2026-05-25 04:12:47] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:47] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:47] >> You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-25 04:12:47] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:47] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:47] ==========================================================
SUCCESS [2026-05-25 04:12:47] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:47] ==========================================================
INFO [2026-05-25 04:12:47] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:12:47] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:47] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
DEBUG [2026-05-25 04:12:47] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:47] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:47] #################################################
INFO [2026-05-25 04:12:47] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:47] #################################################
INFO [2026-05-25 04:12:47] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-25 04:12:47] **** Contig number in your Csv file is 2
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:47] ========================================================
INFO [2026-05-25 04:12:47] >> Contig Name: 'rbcL2'
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:47] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:47] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:48] >> The number of reads detected: 4
SUCCESS [2026-05-25 04:12:48] ==========================================================
SUCCESS [2026-05-25 04:12:48] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:48] ==========================================================
INFO [2026-05-25 04:12:48] >> 4 read(s) created from ABIF file.
INFO [2026-05-25 04:12:48] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:48] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:48] ========================================================
INFO [2026-05-25 04:12:48] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:48] ========================================================
INFO [2026-05-25 04:12:48] >> Contig Name: 'ITS5'
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:48] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:48] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:49] >> The number of reads detected: 4
SUCCESS [2026-05-25 04:12:49] ==========================================================
SUCCESS [2026-05-25 04:12:49] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:49] ==========================================================
INFO [2026-05-25 04:12:49] >> 4 read(s) created from ABIF file.
INFO [2026-05-25 04:12:49] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:49] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:12:49] Aligning consensus reads ...
INFO [2026-05-25 04:12:49] Before building!!
INFO [2026-05-25 04:12:49] After building!!
INFO [2026-05-25 04:12:49] The number of contigs is less than 3 or quality of reads are too low. 'Contigs Tree' cannot be created.
SUCCESS [2026-05-25 04:12:49] #############################################################
SUCCESS [2026-05-25 04:12:49] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:49] #############################################################
INFO [2026-05-25 04:12:49] >> 2 contigs detected from 'csv file'.
INFO [2026-05-25 04:12:49] >> Contig 'rbcL2':
INFO [2026-05-25 04:12:49] >> 2 forward reads.
INFO [2026-05-25 04:12:49] >> 2 reverse reads.
INFO [2026-05-25 04:12:49] >> Contig 'ITS5':
INFO [2026-05-25 04:12:49] >> 2 forward reads.
INFO [2026-05-25 04:12:49] >> 2 reverse reads.
INFO [2026-05-25 04:12:49] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:12:49] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:49] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:49] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:12:49] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e111ef6b7/names_conversion.csv)
WARN [2026-05-25 04:12:49] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e111ef6b7/names_conversion.csv)
WARN [2026-05-25 04:12:49] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e111ef6b7/names_conversion.csv)
WARN [2026-05-25 04:12:49] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e111ef6b7/names_conversion.csv)
WARN [2026-05-25 04:12:49] 'NONEXISTENT_F.ab1' is not in the parent directory.
WARN [2026-05-25 04:12:49] 'NONEXISTENT_R.ab1' is not in the parent directory.
INFO [2026-05-25 04:12:49] #################################################
INFO [2026-05-25 04:12:49] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:49] #################################################
INFO [2026-05-25 04:12:49] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-25 04:12:49] **** Contig number in your Csv file is 2
WARN [2026-05-25 04:12:49] >> Contig 'ghost' has no reads matching any file under ABIF_Directory; skipping.
INFO [2026-05-25 04:12:49] ========================================================
INFO [2026-05-25 04:12:49] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:49] ========================================================
INFO [2026-05-25 04:12:49] >> Contig Name: 'good'
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:49] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:49] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:50] >> The number of reads detected: 4
SUCCESS [2026-05-25 04:12:50] ==========================================================
SUCCESS [2026-05-25 04:12:50] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:50] ==========================================================
INFO [2026-05-25 04:12:50] >> 4 read(s) created from ABIF file.
INFO [2026-05-25 04:12:50] >> 2 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:12:50] >> 2 reads assigned to 'reverse reads' according to 'csv file'.
SUCCESS [2026-05-25 04:12:50] #############################################################
SUCCESS [2026-05-25 04:12:50] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:50] #############################################################
INFO [2026-05-25 04:12:50] >> 1 contigs detected from 'csv file'.
INFO [2026-05-25 04:12:50] >> Contig 'good':
INFO [2026-05-25 04:12:50] >> 2 forward reads.
INFO [2026-05-25 04:12:50] >> 2 reverse reads.
INFO [2026-05-25 04:12:50] >> 4 reads created from ABIF file.
INFO [2026-05-25 04:12:50] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:50] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:50] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:12:50] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-25 04:12:50] #################################################
INFO [2026-05-25 04:12:50] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:50] #################################################
INFO [2026-05-25 04:12:50] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:50] ========================================================
INFO [2026-05-25 04:12:50] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:50] ========================================================
INFO [2026-05-25 04:12:50] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:50] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:50] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:50] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:50] ==========================================================
SUCCESS [2026-05-25 04:12:50] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:50] ==========================================================
INFO [2026-05-25 04:12:50] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:50] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:50] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:50] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:50] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:50] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:50] ========================================================
INFO [2026-05-25 04:12:50] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:50] ========================================================
INFO [2026-05-25 04:12:50] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:51] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:51] ==========================================================
SUCCESS [2026-05-25 04:12:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:51] ==========================================================
INFO [2026-05-25 04:12:51] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:51] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:51] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:51] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:51] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:51] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:51] ==========================================================
SUCCESS [2026-05-25 04:12:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:51] ==========================================================
INFO [2026-05-25 04:12:51] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:51] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:51] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:51] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:51] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:51] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:51] ==========================================================
SUCCESS [2026-05-25 04:12:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:51] ==========================================================
INFO [2026-05-25 04:12:51] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:51] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:51] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:51] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:51] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:51] Aligning consensus reads ...
INFO [2026-05-25 04:12:51] Before building!!
INFO [2026-05-25 04:12:51] After building!!
SUCCESS [2026-05-25 04:12:51] #############################################################
SUCCESS [2026-05-25 04:12:51] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:51] #############################################################
INFO [2026-05-25 04:12:51] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:12:51] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:51] >> 1 forward reads.
INFO [2026-05-25 04:12:51] >> 0 reverse reads.
INFO [2026-05-25 04:12:51] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:51] >> 1 forward reads.
INFO [2026-05-25 04:12:51] >> 0 reverse reads.
INFO [2026-05-25 04:12:51] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:51] >> 1 forward reads.
INFO [2026-05-25 04:12:51] >> 0 reverse reads.
INFO [2026-05-25 04:12:51] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:51] >> 1 forward reads.
INFO [2026-05-25 04:12:51] >> 0 reverse reads.
INFO [2026-05-25 04:12:51] >> 4 reads created from ABIF file.
INFO [2026-05-25 04:12:51] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:51] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:51] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:12:51] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only run.
INFO [2026-05-25 04:12:51] #################################################
INFO [2026-05-25 04:12:51] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:51] #################################################
INFO [2026-05-25 04:12:51] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:51] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:51] ==========================================================
SUCCESS [2026-05-25 04:12:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:51] ==========================================================
INFO [2026-05-25 04:12:51] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:51] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:51] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:51] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:51] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:51] ========================================================
INFO [2026-05-25 04:12:51] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:51] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:51] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:51] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:51] ==========================================================
SUCCESS [2026-05-25 04:12:51] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:51] ==========================================================
INFO [2026-05-25 04:12:51] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:51] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:51] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:51] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:51] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:52] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:52] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:52] ==========================================================
SUCCESS [2026-05-25 04:12:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:52] ==========================================================
INFO [2026-05-25 04:12:52] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:52] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:52] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:52] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:52] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:52] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:52] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:52] ==========================================================
SUCCESS [2026-05-25 04:12:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:52] ==========================================================
INFO [2026-05-25 04:12:52] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:52] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:52] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:52] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:52] >> There is only one read in your SangerContig.
WARN [2026-05-25 04:12:52] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
INFO [2026-05-25 04:12:52] Aligning consensus reads ...
INFO [2026-05-25 04:12:52] Before building!!
INFO [2026-05-25 04:12:52] After building!!
SUCCESS [2026-05-25 04:12:52] #############################################################
SUCCESS [2026-05-25 04:12:52] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:12:52] #############################################################
INFO [2026-05-25 04:12:52] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:12:52] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:12:52] >> 1 forward reads.
INFO [2026-05-25 04:12:52] >> 0 reverse reads.
INFO [2026-05-25 04:12:52] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:12:52] >> 1 forward reads.
INFO [2026-05-25 04:12:52] >> 0 reverse reads.
INFO [2026-05-25 04:12:52] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:12:52] >> 1 forward reads.
INFO [2026-05-25 04:12:52] >> 0 reverse reads.
INFO [2026-05-25 04:12:52] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:12:52] >> 1 forward reads.
INFO [2026-05-25 04:12:52] >> 0 reverse reads.
INFO [2026-05-25 04:12:52] >> 4 reads created from ABIF file.
INFO [2026-05-25 04:12:52] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:52] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:52] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:12:52] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:52] ========================================================
INFO [2026-05-25 04:12:52] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:52] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:52] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:52] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:52] ==========================================================
SUCCESS [2026-05-25 04:12:52] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:52] ==========================================================
INFO [2026-05-25 04:12:52] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:52] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:52] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:52] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:52] >> There is only one read in your SangerContig.
INFO [2026-05-25 04:12:52] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-25 04:12:52] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-25 04:12:52] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:52] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:52] ------------------------------------------------
INFO [2026-05-25 04:12:52] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:52] ------------------------------------------------
INFO [2026-05-25 04:12:52] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:12:52] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:12:52] >> Creating Forward Read raw sangerseq ...
WARN [2026-05-25 04:12:52] >> ABIF 'Achl_ACHLO006-09_1_F.ab1' has no PCON.2 quality block; synthesising flat Phred 30 (MISSING_QUALITY_SCORES_WARN).
INFO [2026-05-25 04:12:52] * Making basecall !!
INFO [2026-05-25 04:12:52] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:52] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:52] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:52] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:52] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:52] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:12:52] ------------------------------------------------
INFO [2026-05-25 04:12:52] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:52] ------------------------------------------------
INFO [2026-05-25 04:12:52] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:12:52] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:12:52] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:12:52] * Making basecall !!
INFO [2026-05-25 04:12:53] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:53] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:53] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:53] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
WARN [2026-05-25 04:12:53] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-25 04:12:53] ========================================================
INFO [2026-05-25 04:12:53] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:53] ========================================================
INFO [2026-05-25 04:12:53] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:53] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:53] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:53] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:53] ==========================================================
SUCCESS [2026-05-25 04:12:53] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:53] ==========================================================
INFO [2026-05-25 04:12:53] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:53] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:53] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:53] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:53] >> There is only one read in your SangerContig.
INFO [2026-05-25 04:12:53] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-25 04:12:53] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-25 04:12:53] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:53] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:53] >>> outputDir : /tmp/RtmpC2hLks/file13c28e3d49c15f
INFO [2026-05-25 04:12:53] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-25 04:12:53] >> Writing alignment to FASTA ...
INFO [2026-05-25 04:12:53] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:12:53] >> Writing consensus read to FASTA ...
INFO [2026-05-25 04:12:53] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-25 04:12:53] >> No 'REGEX_SuffixReverse' supplied; treating as forward-only contig.
INFO [2026-05-25 04:12:53] ========================================================
INFO [2026-05-25 04:12:53] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:53] ========================================================
INFO [2026-05-25 04:12:53] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:53] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:53] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:12:53] >> The number of reads detected: 1
SUCCESS [2026-05-25 04:12:53] ==========================================================
SUCCESS [2026-05-25 04:12:53] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:53] ==========================================================
INFO [2026-05-25 04:12:53] >> 1 read(s) created from ABIF file.
INFO [2026-05-25 04:12:53] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:53] >> 0 reads assigned to 'reverse reads' according to 'regular expression'.
WARN [2026-05-25 04:12:53] >> No 'reverse read' is detected!
WARN [2026-05-25 04:12:53] >> There is only one read in your SangerContig.
INFO [2026-05-25 04:12:53] >> Trimmed by 'M1 - Mott's trimming algorithm'.
WARN [2026-05-25 04:12:53] REGEX_MATCH_WARN
Your 'contigName' and 'REGEX_SuffixReverse' regular expression parameters can not match any reverse reads.
DEBUG [2026-05-25 04:12:53] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:53] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:53] Your input is 'SangerContig' S4 instance
INFO [2026-05-25 04:12:53] >>> outputDir : /tmp/RtmpC2hLks/file13c28e7c843a69
INFO [2026-05-25 04:12:53] Start to write 'Achl_ACHLO006-09' to FASTA format ...
INFO [2026-05-25 04:12:53] >> Writing alignment to FASTA ...
INFO [2026-05-25 04:12:53] >> Writing all single reads to FASTA ...
INFO [2026-05-25 04:12:53] >> Writing consensus read to FASTA ...
INFO [2026-05-25 04:12:53] Finish writing 'Achl_ACHLO006-09' to FASTA format
WARN [2026-05-25 04:12:53] >> Dropping 1 read(s) with trimmed length < 2 bp (MIN_READ_LENGTH_DEFENSIVE_DROP).
WARN [2026-05-25 04:12:53] >> Fewer than 2 usable reads after defensive filter; returning empty consensus.
INFO [2026-05-25 04:12:53] ------------------------------------------------
INFO [2026-05-25 04:12:53] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:53] ------------------------------------------------
INFO [2026-05-25 04:12:53] Forward Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
INFO [2026-05-25 04:12:53] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:53] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:53] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:12:53] ------------------------------------------------
INFO [2026-05-25 04:12:53] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:12:53] ------------------------------------------------
INFO [2026-05-25 04:12:53] Reverse Read: Creating SangerRead from FASTA ...
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:53] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:53] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:12:53] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:53] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:12:53] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:12:54] ========================================================
INFO [2026-05-25 04:12:54] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:54] ========================================================
INFO [2026-05-25 04:12:54] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:54] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:54] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:54] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:54] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:54] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:54] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:54] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:54] ==========================================================
SUCCESS [2026-05-25 04:12:54] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:54] ==========================================================
INFO [2026-05-25 04:12:54] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:54] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:54] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:54] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:54] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:54] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:12:54] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig.
WARN [2026-05-25 04:12:54] 'Achl_ACHLO007-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e57ff03c0/names_conversion.csv)
WARN [2026-05-25 04:12:54] 'Achl_ACHLO040-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e57ff03c0/names_conversion.csv)
WARN [2026-05-25 04:12:54] 'Achl_ACHLO040-09_2_R.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e57ff03c0/names_conversion.csv)
WARN [2026-05-25 04:12:54] 'Achl_ACHLO041-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e57ff03c0/names_conversion.csv)
WARN [2026-05-25 04:12:54] 'Achl_ACHLO041-09_2_R.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e57ff03c0/names_conversion.csv)
WARN [2026-05-25 04:12:54] Read(s) assigned to >1 distinct contig in CSV: 'Achl_ACHLO006-09_1_F.ab1'. Each read must belong to exactly one contig. (READ_ASSIGNED_MULTIPLE_CONTIGS_WARN)
[[1]]
character(0)
[[2]]
character(0)
[[1]]
character(0)
[[2]]
character(0)
INFO [2026-05-25 04:12:55] ========================================================
INFO [2026-05-25 04:12:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:55] ========================================================
INFO [2026-05-25 04:12:55] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:55] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:55] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:55] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:55] ==========================================================
SUCCESS [2026-05-25 04:12:55] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:55] ==========================================================
INFO [2026-05-25 04:12:55] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:55] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:55] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:55] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:55] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:55] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:55] ========================================================
INFO [2026-05-25 04:12:55] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:55] ========================================================
INFO [2026-05-25 04:12:55] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:55] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:55] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:55] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:55] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:56] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:56] ==========================================================
SUCCESS [2026-05-25 04:12:56] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:56] ==========================================================
INFO [2026-05-25 04:12:56] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:56] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:56] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:56] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:56] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:56] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:56] ========================================================
INFO [2026-05-25 04:12:56] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:56] ========================================================
INFO [2026-05-25 04:12:56] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:56] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:56] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:56] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:56] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:56] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:57] ==========================================================
SUCCESS [2026-05-25 04:12:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:57] ==========================================================
INFO [2026-05-25 04:12:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:57] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:57] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:57] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:57] ========================================================
INFO [2026-05-25 04:12:57] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:57] ========================================================
INFO [2026-05-25 04:12:57] >> Contig Name: 'Achl_ACHLO006-09'
INFO [2026-05-25 04:12:57] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:57] >> Your contig name is Achl_ACHLO006-09
SUCCESS [2026-05-25 04:12:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:57] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:57] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:57] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:57] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:57] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:57] ==========================================================
SUCCESS [2026-05-25 04:12:57] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:57] ==========================================================
INFO [2026-05-25 04:12:57] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:57] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:57] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:57] >> Trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:12:57] >> For more information, please run 'object'
DEBUG [2026-05-25 04:12:57] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:12:58] #################################################
INFO [2026-05-25 04:12:58] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:12:58] #################################################
INFO [2026-05-25 04:12:58] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:12:58] ========================================================
INFO [2026-05-25 04:12:58] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:58] ========================================================
INFO [2026-05-25 04:12:58] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:58] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:58] ==========================================================
SUCCESS [2026-05-25 04:12:58] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:58] ==========================================================
INFO [2026-05-25 04:12:58] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:58] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:58] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:58] ========================================================
INFO [2026-05-25 04:12:58] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:58] ========================================================
INFO [2026-05-25 04:12:58] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:58] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:58] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:59] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:12:59] ==========================================================
SUCCESS [2026-05-25 04:12:59] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:12:59] ==========================================================
INFO [2026-05-25 04:12:59] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:12:59] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:12:59] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:12:59] ========================================================
INFO [2026-05-25 04:12:59] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:12:59] ========================================================
INFO [2026-05-25 04:12:59] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:12:59] --------------------------------------------------------
SUCCESS [2026-05-25 04:12:59] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:12:59] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:00] ==========================================================
SUCCESS [2026-05-25 04:13:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:00] ==========================================================
INFO [2026-05-25 04:13:00] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:00] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:00] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:00] ========================================================
INFO [2026-05-25 04:13:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:00] ========================================================
INFO [2026-05-25 04:13:00] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:00] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:00] ==========================================================
SUCCESS [2026-05-25 04:13:00] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:00] ==========================================================
INFO [2026-05-25 04:13:00] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:00] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:00] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:00] Aligning consensus reads ...
INFO [2026-05-25 04:13:00] Before building!!
INFO [2026-05-25 04:13:00] After building!!
SUCCESS [2026-05-25 04:13:00] #############################################################
SUCCESS [2026-05-25 04:13:00] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:00] #############################################################
INFO [2026-05-25 04:13:00] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:00] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:00] >> 1 forward reads.
INFO [2026-05-25 04:13:00] >> 1 reverse reads.
INFO [2026-05-25 04:13:00] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:00] >> 1 forward reads.
INFO [2026-05-25 04:13:00] >> 1 reverse reads.
INFO [2026-05-25 04:13:00] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:00] >> 1 forward reads.
INFO [2026-05-25 04:13:00] >> 1 reverse reads.
INFO [2026-05-25 04:13:00] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:00] >> 1 forward reads.
INFO [2026-05-25 04:13:00] >> 1 reverse reads.
INFO [2026-05-25 04:13:00] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:13:00] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:00] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:00] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:00] #################################################
INFO [2026-05-25 04:13:00] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:13:00] #################################################
INFO [2026-05-25 04:13:00] **** You are using Regular Expression Method to group reads in FASTA file (No CSV file)!
INFO [2026-05-25 04:13:00] ========================================================
INFO [2026-05-25 04:13:00] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:00] ========================================================
INFO [2026-05-25 04:13:00] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] >> 'Achl_ACHLO006-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:00] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:00] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:13:00] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:01] ==========================================================
SUCCESS [2026-05-25 04:13:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:01] ==========================================================
INFO [2026-05-25 04:13:01] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:13:01] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:01] ==========================================================
SUCCESS [2026-05-25 04:13:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:01] ==========================================================
INFO [2026-05-25 04:13:01] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:13:01] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:01] ==========================================================
SUCCESS [2026-05-25 04:13:01] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:01] ==========================================================
INFO [2026-05-25 04:13:01] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:01] ========================================================
INFO [2026-05-25 04:13:01] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:01] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:01] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:13:01] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:02] ==========================================================
SUCCESS [2026-05-25 04:13:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:02] ==========================================================
INFO [2026-05-25 04:13:02] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:13:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:02] Aligning consensus reads ...
INFO [2026-05-25 04:13:02] Before building!!
INFO [2026-05-25 04:13:02] After building!!
SUCCESS [2026-05-25 04:13:02] #############################################################
SUCCESS [2026-05-25 04:13:02] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:02] #############################################################
INFO [2026-05-25 04:13:02] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:02] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:02] >> 1 forward reads.
INFO [2026-05-25 04:13:02] >> 1 reverse reads.
INFO [2026-05-25 04:13:02] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:02] >> 1 forward reads.
INFO [2026-05-25 04:13:02] >> 1 reverse reads.
INFO [2026-05-25 04:13:02] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:02] >> 1 forward reads.
INFO [2026-05-25 04:13:02] >> 1 reverse reads.
INFO [2026-05-25 04:13:02] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:02] >> 1 forward reads.
INFO [2026-05-25 04:13:02] >> 1 reverse reads.
INFO [2026-05-25 04:13:02] >> 8 reads created from FASTA file.
DEBUG [2026-05-25 04:13:02] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:02] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:02] #################################################
INFO [2026-05-25 04:13:02] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:13:02] #################################################
INFO [2026-05-25 04:13:02] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:13:02] ========================================================
INFO [2026-05-25 04:13:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:02] ========================================================
INFO [2026-05-25 04:13:02] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:02] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:02] ==========================================================
SUCCESS [2026-05-25 04:13:02] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:02] ==========================================================
INFO [2026-05-25 04:13:02] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:02] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:02] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:02] ========================================================
INFO [2026-05-25 04:13:02] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:02] ========================================================
INFO [2026-05-25 04:13:02] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:02] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:02] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:03] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:03] ==========================================================
SUCCESS [2026-05-25 04:13:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:03] ==========================================================
INFO [2026-05-25 04:13:03] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:03] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:03] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:03] ========================================================
INFO [2026-05-25 04:13:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:03] ========================================================
INFO [2026-05-25 04:13:03] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:03] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:03] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:03] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:03] ==========================================================
SUCCESS [2026-05-25 04:13:03] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:03] ==========================================================
INFO [2026-05-25 04:13:03] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:03] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:03] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:03] ========================================================
INFO [2026-05-25 04:13:03] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:03] ========================================================
INFO [2026-05-25 04:13:03] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:04] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:04] ==========================================================
SUCCESS [2026-05-25 04:13:04] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:04] ==========================================================
INFO [2026-05-25 04:13:04] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:04] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:04] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:04] Aligning consensus reads ...
INFO [2026-05-25 04:13:04] Before building!!
INFO [2026-05-25 04:13:04] After building!!
SUCCESS [2026-05-25 04:13:04] #############################################################
SUCCESS [2026-05-25 04:13:04] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:04] #############################################################
INFO [2026-05-25 04:13:04] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:04] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:04] >> 1 forward reads.
INFO [2026-05-25 04:13:04] >> 1 reverse reads.
INFO [2026-05-25 04:13:04] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:04] >> 1 forward reads.
INFO [2026-05-25 04:13:04] >> 1 reverse reads.
INFO [2026-05-25 04:13:04] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:04] >> 1 forward reads.
INFO [2026-05-25 04:13:04] >> 1 reverse reads.
INFO [2026-05-25 04:13:04] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:04] >> 1 forward reads.
INFO [2026-05-25 04:13:04] >> 1 reverse reads.
INFO [2026-05-25 04:13:04] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:13:04] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:04] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:04] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:04] * Making basecall !!
INFO [2026-05-25 04:13:04] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:04] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:04] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:04] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:04] * Making basecall !!
INFO [2026-05-25 04:13:04] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:04] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:04] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:04] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:04] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:04] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:04] ------------------------------------------------
INFO [2026-05-25 04:13:04] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:04] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:04] * Making basecall !!
INFO [2026-05-25 04:13:05] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:05] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:05] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:05] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:05] ------------------------------------------------
INFO [2026-05-25 04:13:05] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:05] ------------------------------------------------
INFO [2026-05-25 04:13:05] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:05] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:05] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:05] * Making basecall !!
INFO [2026-05-25 04:13:05] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:05] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:05] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:05] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:05] ------------------------------------------------
INFO [2026-05-25 04:13:05] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:05] ------------------------------------------------
INFO [2026-05-25 04:13:05] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:05] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:05] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:05] * Making basecall !!
INFO [2026-05-25 04:13:05] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:05] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:05] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:05] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:05] #################################################
INFO [2026-05-25 04:13:05] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:13:05] #################################################
INFO [2026-05-25 04:13:05] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:13:05] ========================================================
INFO [2026-05-25 04:13:05] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:05] ========================================================
INFO [2026-05-25 04:13:05] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:05] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:05] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:05] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:05] ==========================================================
SUCCESS [2026-05-25 04:13:05] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:05] ==========================================================
INFO [2026-05-25 04:13:06] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:06] ========================================================
INFO [2026-05-25 04:13:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:06] ========================================================
INFO [2026-05-25 04:13:06] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:06] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:06] ==========================================================
SUCCESS [2026-05-25 04:13:06] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:06] ==========================================================
INFO [2026-05-25 04:13:06] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:06] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:06] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:06] ========================================================
INFO [2026-05-25 04:13:06] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:06] ========================================================
INFO [2026-05-25 04:13:06] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:06] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:06] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:06] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:07] ==========================================================
SUCCESS [2026-05-25 04:13:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:07] ==========================================================
INFO [2026-05-25 04:13:07] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:07] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:07] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:07] ========================================================
INFO [2026-05-25 04:13:07] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:07] ========================================================
INFO [2026-05-25 04:13:07] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:07] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:07] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:07] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:07] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:07] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:07] ==========================================================
SUCCESS [2026-05-25 04:13:07] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:07] ==========================================================
INFO [2026-05-25 04:13:07] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:07] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:07] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:07] Aligning consensus reads ...
INFO [2026-05-25 04:13:07] Before building!!
INFO [2026-05-25 04:13:07] After building!!
SUCCESS [2026-05-25 04:13:07] #############################################################
SUCCESS [2026-05-25 04:13:07] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:07] #############################################################
INFO [2026-05-25 04:13:07] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:07] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:07] >> 1 forward reads.
INFO [2026-05-25 04:13:07] >> 1 reverse reads.
INFO [2026-05-25 04:13:07] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:07] >> 1 forward reads.
INFO [2026-05-25 04:13:07] >> 1 reverse reads.
INFO [2026-05-25 04:13:07] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:07] >> 1 forward reads.
INFO [2026-05-25 04:13:07] >> 1 reverse reads.
INFO [2026-05-25 04:13:07] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:07] >> 1 forward reads.
INFO [2026-05-25 04:13:07] >> 1 reverse reads.
INFO [2026-05-25 04:13:07] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:13:07] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:07] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:07] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:12] Aligning consensus reads ...
INFO [2026-05-25 04:13:12] Before building!!
INFO [2026-05-25 04:13:12] After building!!
INFO [2026-05-25 04:13:17] Aligning consensus reads ...
INFO [2026-05-25 04:13:17] Before building!!
INFO [2026-05-25 04:13:17] After building!!
INFO [2026-05-25 04:13:22] Aligning consensus reads ...
INFO [2026-05-25 04:13:22] Before building!!
INFO [2026-05-25 04:13:22] After building!!
INFO [2026-05-25 04:13:26] Aligning consensus reads ...
INFO [2026-05-25 04:13:26] Before building!!
INFO [2026-05-25 04:13:26] After building!!
INFO [2026-05-25 04:13:31] Aligning consensus reads ...
INFO [2026-05-25 04:13:31] Before building!!
INFO [2026-05-25 04:13:31] After building!!
INFO [2026-05-25 04:13:31] ------------------------------------------------
INFO [2026-05-25 04:13:31] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:31] ------------------------------------------------
INFO [2026-05-25 04:13:31] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:31] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:31] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:31] * Making basecall !!
INFO [2026-05-25 04:13:31] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:31] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:31] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:31] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:31] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:31] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:31] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:32] ------------------------------------------------
INFO [2026-05-25 04:13:32] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:32] ------------------------------------------------
INFO [2026-05-25 04:13:32] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:32] >> Creating Reverse Read raw abif ...
INFO [2026-05-25 04:13:32] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-25 04:13:32] * Making basecall !!
INFO [2026-05-25 04:13:32] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:32] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:32] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:32] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:32] ------------------------------------------------
INFO [2026-05-25 04:13:32] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:32] ------------------------------------------------
INFO [2026-05-25 04:13:32] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:32] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:32] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:32] * Making basecall !!
INFO [2026-05-25 04:13:32] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:32] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:32] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:32] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:13:32] #################################################
INFO [2026-05-25 04:13:32] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:13:32] #################################################
INFO [2026-05-25 04:13:32] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:13:32] ========================================================
INFO [2026-05-25 04:13:32] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:32] ========================================================
INFO [2026-05-25 04:13:32] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:32] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:32] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:33] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:33] ==========================================================
SUCCESS [2026-05-25 04:13:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:33] ==========================================================
INFO [2026-05-25 04:13:33] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:33] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:33] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:33] ========================================================
INFO [2026-05-25 04:13:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:33] ========================================================
INFO [2026-05-25 04:13:33] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:33] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:33] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:33] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:33] ==========================================================
SUCCESS [2026-05-25 04:13:33] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:33] ==========================================================
INFO [2026-05-25 04:13:33] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:33] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:33] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:33] ========================================================
INFO [2026-05-25 04:13:33] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:33] ========================================================
INFO [2026-05-25 04:13:33] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:34] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:34] ==========================================================
SUCCESS [2026-05-25 04:13:34] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:34] ==========================================================
INFO [2026-05-25 04:13:34] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:34] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:34] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:34] ========================================================
INFO [2026-05-25 04:13:34] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:34] ========================================================
INFO [2026-05-25 04:13:34] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:34] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:34] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:34] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:35] ==========================================================
SUCCESS [2026-05-25 04:13:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:35] ==========================================================
INFO [2026-05-25 04:13:35] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:35] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:35] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:35] Aligning consensus reads ...
INFO [2026-05-25 04:13:35] Before building!!
INFO [2026-05-25 04:13:35] After building!!
SUCCESS [2026-05-25 04:13:35] #############################################################
SUCCESS [2026-05-25 04:13:35] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:35] #############################################################
INFO [2026-05-25 04:13:35] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:35] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:35] >> 1 forward reads.
INFO [2026-05-25 04:13:35] >> 1 reverse reads.
INFO [2026-05-25 04:13:35] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:35] >> 1 forward reads.
INFO [2026-05-25 04:13:35] >> 1 reverse reads.
INFO [2026-05-25 04:13:35] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:35] >> 1 forward reads.
INFO [2026-05-25 04:13:35] >> 1 reverse reads.
INFO [2026-05-25 04:13:35] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:35] >> 1 forward reads.
INFO [2026-05-25 04:13:35] >> 1 reverse reads.
INFO [2026-05-25 04:13:35] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:13:35] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:35] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:35] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:35] #################################################
INFO [2026-05-25 04:13:35] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:13:35] #################################################
INFO [2026-05-25 04:13:35] >> You are using Regular Expression Method to group AB1 files!
INFO [2026-05-25 04:13:35] ========================================================
INFO [2026-05-25 04:13:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:35] ========================================================
INFO [2026-05-25 04:13:35] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:35] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:35] ==========================================================
SUCCESS [2026-05-25 04:13:35] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:35] ==========================================================
INFO [2026-05-25 04:13:35] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:35] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:35] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:35] ========================================================
INFO [2026-05-25 04:13:35] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:35] ========================================================
INFO [2026-05-25 04:13:35] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:35] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:35] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:35] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:36] ==========================================================
SUCCESS [2026-05-25 04:13:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:36] ==========================================================
INFO [2026-05-25 04:13:36] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:36] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:36] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:36] ========================================================
INFO [2026-05-25 04:13:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:36] ========================================================
INFO [2026-05-25 04:13:36] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:36] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:36] ==========================================================
SUCCESS [2026-05-25 04:13:36] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:36] ==========================================================
INFO [2026-05-25 04:13:36] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:36] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:36] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:36] ========================================================
INFO [2026-05-25 04:13:36] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:13:36] ========================================================
INFO [2026-05-25 04:13:36] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:36] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:36] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:13:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:37] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:13:37] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:13:37] ==========================================================
SUCCESS [2026-05-25 04:13:37] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:13:37] ==========================================================
INFO [2026-05-25 04:13:37] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:13:37] >> 1 reads assigned to 'forward reads' according to 'regular expression'.
INFO [2026-05-25 04:13:37] >> 1 reads assigned to 'reverse reads' according to 'regular expression'.
INFO [2026-05-25 04:13:37] Aligning consensus reads ...
INFO [2026-05-25 04:13:37] Before building!!
INFO [2026-05-25 04:13:37] After building!!
SUCCESS [2026-05-25 04:13:37] #############################################################
SUCCESS [2026-05-25 04:13:37] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:13:37] #############################################################
INFO [2026-05-25 04:13:37] >> 4 contigs detected from 'regular expression'.
INFO [2026-05-25 04:13:37] >> Contig 'Achl_ACHLO006-09':
INFO [2026-05-25 04:13:37] >> 1 forward reads.
INFO [2026-05-25 04:13:37] >> 1 reverse reads.
INFO [2026-05-25 04:13:37] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:13:37] >> 1 forward reads.
INFO [2026-05-25 04:13:37] >> 1 reverse reads.
INFO [2026-05-25 04:13:37] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:13:37] >> 1 forward reads.
INFO [2026-05-25 04:13:37] >> 1 reverse reads.
INFO [2026-05-25 04:13:37] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:13:37] >> 1 forward reads.
INFO [2026-05-25 04:13:37] >> 1 reverse reads.
INFO [2026-05-25 04:13:37] >> 8 reads created from ABIF file.
INFO [2026-05-25 04:13:37] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:37] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:37] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:13:37] ------------------------------------------------
INFO [2026-05-25 04:13:37] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:13:37] ------------------------------------------------
INFO [2026-05-25 04:13:37] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:13:37] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:13:37] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:13:37] * Making basecall !!
INFO [2026-05-25 04:13:37] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:13:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:37] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:13:37] --------------------------------------------------------
SUCCESS [2026-05-25 04:13:37] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:13:37] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:13:37] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:13:37] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
================================================================================
Time difference of 0.03 secs
================================================================================
Time difference of 0.03 secs
================================================================================
Time difference of 0.03 secs
================================================================================
Time difference of 0.03 secs
INFO [2026-05-25 04:13:45] Aligning consensus reads ...
================================================================================
Time difference of 0.08 secs
================================================================================
Time difference of 0.06 secs
================================================================================
Time difference of 0.11 secs
================================================================================
Time difference of 0.14 secs
INFO [2026-05-25 04:14:01] Aligning consensus reads ...
================================================================================
Time difference of 0.08 secs
================================================================================
Time difference of 0.05 secs
INFO [2026-05-25 04:14:12] * Making basecall !!
INFO [2026-05-25 04:14:12] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:12] * Making basecall !!
INFO [2026-05-25 04:14:12] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:13] * Making basecall !!
INFO [2026-05-25 04:14:13] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:13] * Making basecall !!
INFO [2026-05-25 04:14:13] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:14] * Making basecall !!
INFO [2026-05-25 04:14:14] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:18] >>> outputDir : /tmp/RtmpC2hLks
INFO [2026-05-25 04:14:18] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//Allolobophora_chlorotica/ACHLO/Achl_ACHLO006-09_1_F.ab1' to FASTA format ...
INFO [2026-05-25 04:14:18] >> '/tmp/RtmpC2hLks/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-25 04:14:18] >>> outputDir : /tmp/RtmpC2hLks
INFO [2026-05-25 04:14:18] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_1_F.fa' to FASTA format ...
INFO [2026-05-25 04:14:18] >> '/tmp/RtmpC2hLks/Achl_ACHLO006-09_1_F.fa' is written
INFO [2026-05-25 04:14:18] >>> outputDir : /tmp/RtmpC2hLks
INFO [2026-05-25 04:14:18] Start writing '/home/biocbuild/bbs-3.24-bioc/R/site-library/sangeranalyseR/extdata//fasta/SangerRead/Achl_ACHLO006-09_2_R.fa' to FASTA format ...
INFO [2026-05-25 04:14:18] >> '/tmp/RtmpC2hLks/Achl_ACHLO006-09_2_R.fa' is written
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:18] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:18] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:14:18] * Making basecall !!
INFO [2026-05-25 04:14:18] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:14:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:18] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:14:18] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:14:18] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:18] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] >> Reverse Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:18] >> Creating Reverse Read raw abif ...
INFO [2026-05-25 04:14:18] >> Creating Reverse Read raw sangerseq ...
INFO [2026-05-25 04:14:18] * Making basecall !!
INFO [2026-05-25 04:14:18] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:14:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:18] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:18] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:18] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:14:18] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:14:18] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:18] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:18] ------------------------------------------------
INFO [2026-05-25 04:14:18] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:18] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:18] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:14:18] * Making basecall !!
INFO [2026-05-25 04:14:19] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:14:19] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw sangerseq ...
INFO [2026-05-25 04:14:19] * Making basecall !!
INFO [2026-05-25 04:14:19] * Updating slots in 'SangerRead' instance !!
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] >> 'Achl_ACHLO006-09_1_F.ab1' is created (Forward Read; ABIF).
INFO [2026-05-25 04:14:19] >> Read is trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-25 04:14:19] FILE_TYPE_ERROR
'/tmp/RtmpC2hLks/file13c28e4361db1f/Sanger_all_reads.Xfa' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:19] FILE_TYPE_ERROR
'/tmp/RtmpC2hLks/file13c28e2d14a611/Achl_ACHLO006-09_1_F.Xab1' file extension must be '.ab1'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-25 04:14:19] FILE_TYPE_ERROR
'/tmp/RtmpC2hLks/file13c28e4b0878f9/Achl_ACHLO006-09_1_F.ab2' file extension must be '.ab1'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
ERROR [2026-05-25 04:14:19] FILE_TYPE_ERROR
'/tmp/RtmpC2hLks/file13c28e2ee9608a/Sanger_all_reads.fast' file extension must be '.fa' or '.fasta'.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:19] FILE_NOT_EXIST_ERROR
'/no/such/file_1_F.ab1' file does not exist.
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the result of the Sanger read
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] -------- Creating 'SangerRead' instance --------
INFO [2026-05-25 04:14:19] ------------------------------------------------
INFO [2026-05-25 04:14:19] >> Forward Read: Creating abif & sangerseq ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw abif ...
INFO [2026-05-25 04:14:19] >> Creating Forward Read raw sangerseq ...
ERROR [2026-05-25 04:14:19] CSV_MISMATCH_ERROR
'contig' is not in the csv file (/tmp/RtmpC2hLks/file13c28e1d6c7e07/missing_contig.csv)
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:19] CSV_MISMATCH_ERROR
'direction' is not in the csv file (/tmp/RtmpC2hLks/file13c28e7af3fc2d/missing_direction.csv)
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:19] CSV_MISMATCH_ERROR
'reads' is not in the csv file (/tmp/RtmpC2hLks/file13c28e7c79ea51/missing_reads.csv)
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:19] CSV_VALUE_ERROR
In the 'direction' column of your CSV file, you can only have 'F' and 'R'
DEBUG [2026-05-25 04:14:19] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:19] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:14:19] 'Achl_ACHLO006-09_1_F.ab1' is not in the csv file (/tmp/RtmpC2hLks/file13c28e7b713554/mismatched_names_conversion.csv)
WARN [2026-05-25 04:14:19] 'DOES_NOT_EXIST.ab1' is not in the parent directory.
INFO [2026-05-25 04:14:19] #################################################
INFO [2026-05-25 04:14:19] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:14:19] #################################################
INFO [2026-05-25 04:14:19] **** You are using CSV Name Conversion Method to group AB1 files!
INFO [2026-05-25 04:14:19] **** Contig number in your Csv file is 4
INFO [2026-05-25 04:14:19] ========================================================
INFO [2026-05-25 04:14:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:19] ========================================================
INFO [2026-05-25 04:14:19] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] >> 'Achl_ACHLO006-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:14:19] >> The number of reads detected: 1
WARN [2026-05-25 04:14:19] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-25 04:14:19] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-25 04:14:19] ========================================================
INFO [2026-05-25 04:14:19] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:19] ========================================================
INFO [2026-05-25 04:14:19] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:14:19] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:19] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] >> 'Achl_ACHLO007-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] >> 'Achl_ACHLO007-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:14:20] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:20] ==========================================================
SUCCESS [2026-05-25 04:14:20] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:20] ==========================================================
INFO [2026-05-25 04:14:20] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:14:20] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:20] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:20] ========================================================
INFO [2026-05-25 04:14:20] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:20] ========================================================
INFO [2026-05-25 04:14:20] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] >> 'Achl_ACHLO040-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:20] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:20] >> 'Achl_ACHLO040-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:14:20] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:21] ==========================================================
SUCCESS [2026-05-25 04:14:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:21] ==========================================================
INFO [2026-05-25 04:14:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:14:21] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:21] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] >> 'Achl_ACHLO041-09_1_F.ab1' is created (Forward Read; ABIF).
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] >> 'Achl_ACHLO041-09_2_R.ab1' is created (Reverse Read; ABIF).
INFO [2026-05-25 04:14:21] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:21] ==========================================================
SUCCESS [2026-05-25 04:14:21] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:21] ==========================================================
INFO [2026-05-25 04:14:21] >> 2 read(s) created from ABIF file.
INFO [2026-05-25 04:14:21] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:21] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:21] Aligning consensus reads ...
INFO [2026-05-25 04:14:21] Before building!!
INFO [2026-05-25 04:14:21] After building!!
SUCCESS [2026-05-25 04:14:21] #############################################################
SUCCESS [2026-05-25 04:14:21] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:14:21] #############################################################
INFO [2026-05-25 04:14:21] >> 3 contigs detected from 'csv file'.
INFO [2026-05-25 04:14:21] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:14:21] >> 1 forward reads.
INFO [2026-05-25 04:14:21] >> 1 reverse reads.
INFO [2026-05-25 04:14:21] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:14:21] >> 1 forward reads.
INFO [2026-05-25 04:14:21] >> 1 reverse reads.
INFO [2026-05-25 04:14:21] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:14:21] >> 1 forward reads.
INFO [2026-05-25 04:14:21] >> 1 reverse reads.
INFO [2026-05-25 04:14:21] >> 6 reads created from ABIF file.
INFO [2026-05-25 04:14:21] >> Reads are trimmed by 'M1 - Mott's trimming algorithm'.
DEBUG [2026-05-25 04:14:21] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:21] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
WARN [2026-05-25 04:14:21] 'Achl_ACHLO006-09_1_F' is not in the parent directory.
INFO [2026-05-25 04:14:21] #################################################
INFO [2026-05-25 04:14:21] #### Start creating SangerAlignment instance ####
INFO [2026-05-25 04:14:21] #################################################
INFO [2026-05-25 04:14:21] **** You are using CSV Name Conversion Method to group reads in FASTA file (with Csv file)!
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] >> Contig Name: 'Achl_ACHLO006-09'
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] >> 'Achl_ACHLO006-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:14:21] >> The number of reads detected: 1
WARN [2026-05-25 04:14:21] CSV_MATCH_WARN
The names of forward reads in your 'CSV_NamesConversion' CSV file do not match any forward reads.
ERROR [2026-05-25 04:14:21] READ_NUMBER_ERROR
The number of your total reads is 1.
Number of total reads has to be equal or more than 2 ('minReadsNum' that you set)
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:21] ========================================================
INFO [2026-05-25 04:14:21] >> Contig Name: 'Achl_ACHLO007-09'
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] >> 'Achl_ACHLO007-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:21] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:21] >> 'Achl_ACHLO007-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:14:21] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:22] ==========================================================
SUCCESS [2026-05-25 04:14:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:22] ==========================================================
INFO [2026-05-25 04:14:22] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] ========================================================
INFO [2026-05-25 04:14:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:22] ========================================================
INFO [2026-05-25 04:14:22] >> Contig Name: 'Achl_ACHLO040-09'
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] >> 'Achl_ACHLO040-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] >> 'Achl_ACHLO040-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:14:22] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:22] ==========================================================
SUCCESS [2026-05-25 04:14:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:22] ==========================================================
INFO [2026-05-25 04:14:22] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] ========================================================
INFO [2026-05-25 04:14:22] ================ Creating 'SangerContig' ===============
INFO [2026-05-25 04:14:22] ========================================================
INFO [2026-05-25 04:14:22] >> Contig Name: 'Achl_ACHLO041-09'
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] >> 'Achl_ACHLO041-09_1_F' is created (Forward Read; FASTA).
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] -------- 'SangerRead' S4 instance is created !! --------
SUCCESS [2026-05-25 04:14:22] --------------------------------------------------------
SUCCESS [2026-05-25 04:14:22] >> 'Achl_ACHLO041-09_2_R' is created (Reverse Read; FASTA).
INFO [2026-05-25 04:14:22] >> The number of reads detected: 2
SUCCESS [2026-05-25 04:14:22] ==========================================================
SUCCESS [2026-05-25 04:14:22] ======== 'SangerContig' S4 instance is created !! ========
SUCCESS [2026-05-25 04:14:22] ==========================================================
INFO [2026-05-25 04:14:22] >> 2 read(s) created from FASTA file.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'forward reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] >> 1 reads assigned to 'reverse reads' according to 'csv file'.
INFO [2026-05-25 04:14:22] Aligning consensus reads ...
INFO [2026-05-25 04:14:22] Before building!!
INFO [2026-05-25 04:14:22] After building!!
SUCCESS [2026-05-25 04:14:22] #############################################################
SUCCESS [2026-05-25 04:14:22] ######## 'SangerAlignment' S4 instance is created !! ########
SUCCESS [2026-05-25 04:14:22] #############################################################
INFO [2026-05-25 04:14:22] >> 3 contigs detected from 'csv file'.
INFO [2026-05-25 04:14:22] >> Contig 'Achl_ACHLO007-09':
INFO [2026-05-25 04:14:22] >> 1 forward reads.
INFO [2026-05-25 04:14:22] >> 1 reverse reads.
INFO [2026-05-25 04:14:22] >> Contig 'Achl_ACHLO040-09':
INFO [2026-05-25 04:14:22] >> 1 forward reads.
INFO [2026-05-25 04:14:22] >> 1 reverse reads.
INFO [2026-05-25 04:14:22] >> Contig 'Achl_ACHLO041-09':
INFO [2026-05-25 04:14:22] >> 1 forward reads.
INFO [2026-05-25 04:14:22] >> 1 reverse reads.
INFO [2026-05-25 04:14:22] >> 6 reads created from FASTA file.
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:22] PARAMETER_RANGE_ERROR
'M1TrimmingCutoff' must be between 0 and 1.
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:22] PARAMETER_VALUE_ERROR
'TrimmingMethod' must be 'M1' or 'M2'.
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:22] PARAMETER_TYPE_ERROR
'processorsNum' must be numeric
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:22] PARAMETER_RANGE_ERROR
'signalRatioCutoff' must be between 0 and 1.
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:22] PARAMETER_VALUE_ERROR
'inputSource' must be one of: 'ABIF', 'FASTA'.
DEBUG [2026-05-25 04:14:22] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:22] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:23] PARAMETER_VALUE_ERROR
'processMethod' must be one of: 'REGEX', 'CSV'.
DEBUG [2026-05-25 04:14:23] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:23] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:23] PARAMETER_VALUE_ERROR
'acceptStopCodons' must be 'TRUE' or 'FALSE'
DEBUG [2026-05-25 04:14:23] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:23] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:23] PARAMETER_VALUE_ERROR
'readingFrame' must be 1, 2, or 3.
DEBUG [2026-05-25 04:14:23] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:23] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:23] PARAMETER_RANGE_ERROR
'minFractionCall' must be between 0 and 1.
DEBUG [2026-05-25 04:14:23] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:23] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
ERROR [2026-05-25 04:14:23] PARAMETER_VALUE_ERROR
'minReadsNum' cannot be zero.
DEBUG [2026-05-25 04:14:23] >> For more information, please run 'object'.
DEBUG [2026-05-25 04:14:23] >> Run 'object@objectResults@readResultTable' to check the results of each Sanger reads
INFO [2026-05-25 04:14:23] Aligning consensus reads ...
================================================================================
Time difference of 0.03 secs
INFO [2026-05-25 04:14:25] * Making basecall !!
INFO [2026-05-25 04:14:25] * Updating slots in 'SangerRead' instance !!
INFO [2026-05-25 04:14:25] * Making basecall !!
INFO [2026-05-25 04:14:25] * Updating slots in 'SangerRead' instance !!
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-LazyAA-Reports.R:65:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1447 ]
>
> proc.time()
user system elapsed
206.779 12.519 227.582
sangeranalyseR.Rcheck/sangeranalyseR-Ex.timings
| name | user | system | elapsed | |
| ChromatogramParam-class | 0.004 | 0.000 | 0.004 | |
| MakeBaseCalls-methods | 0.419 | 0.047 | 0.466 | |
| ObjectResults-class | 0.001 | 0.000 | 0.002 | |
| QualityReport-class-qualityBasePlot | 0.001 | 0.000 | 0.002 | |
| QualityReport-class-updateQualityParam | 0.003 | 0.001 | 0.006 | |
| QualityReport-class | 0.192 | 0.003 | 0.196 | |
| SangerAlignment-class-generateReportSA | 0.109 | 0.009 | 0.118 | |
| SangerAlignment-class-launchAppSA | 0.131 | 0.005 | 0.136 | |
| SangerAlignment-class-updateQualityParam | 0.112 | 0.003 | 0.115 | |
| SangerAlignment-class-writeFastaSA | 0.137 | 0.004 | 0.142 | |
| SangerAlignment-class | 36.794 | 9.772 | 43.660 | |
| SangerAlignment | 8.334 | 2.623 | 10.178 | |
| SangerContig-class-generateReportSC | 0.048 | 0.004 | 0.052 | |
| SangerContig-class-launchAppSC | 0.055 | 0.007 | 0.062 | |
| SangerContig-class-readTable | 0.081 | 0.006 | 0.087 | |
| SangerContig-class-updateQualityParam | 0.050 | 0.000 | 0.049 | |
| SangerContig-class-writeFastaSC | 0.079 | 0.010 | 0.089 | |
| SangerContig-class | 8.795 | 2.384 | 10.492 | |
| SangerContig | 0.486 | 0.099 | 0.585 | |
| SangerRead-class-MakeBaseCalls | 0.294 | 0.007 | 0.301 | |
| SangerRead-class-generateReportSR | 0.035 | 0.002 | 0.037 | |
| SangerRead-class-qualityBasePlot | 0.037 | 0.001 | 0.038 | |
| SangerRead-class-readTable | 0.085 | 0.003 | 0.088 | |
| SangerRead-class-updateQualityParam | 0.270 | 0.026 | 0.296 | |
| SangerRead-class-writeFastaSR | 0.050 | 0.002 | 0.052 | |
| SangerRead-class | 0.571 | 0.023 | 0.594 | |
| SangerRead | 0.174 | 0.013 | 0.188 | |
| chromatogram_overwrite | 0.037 | 0.002 | 0.039 | |
| chromatogram_plotly | 0.038 | 0.000 | 0.038 | |
| generateReport | 0.199 | 0.013 | 0.212 | |
| generateReportSA-methods | 0.111 | 0.008 | 0.118 | |
| generateReportSC-methods | 0.049 | 0.001 | 0.050 | |
| generateReportSR-methods | 0.037 | 0.001 | 0.038 | |
| globalTrimApp | 0.000 | 0.000 | 0.001 | |
| launchApp | 0.181 | 0.010 | 0.191 | |
| launchAppSA-methods | 0.114 | 0.007 | 0.121 | |
| launchAppSC-methods | 0.049 | 0.002 | 0.051 | |
| primaryAASeqS1-methods | 0.041 | 0.002 | 0.043 | |
| primaryAASeqS2-methods | 0.036 | 0.004 | 0.040 | |
| primaryAASeqS3-methods | 0.038 | 0.001 | 0.040 | |
| qualityBasePlot-methods | 0.339 | 0.036 | 0.376 | |
| readTable-methods | 0.085 | 0.004 | 0.089 | |
| updateQualityParam-methods | 0.200 | 0.009 | 0.208 | |
| writeFasta | 0.199 | 0.008 | 0.207 | |
| writeFastaSA-methods | 0.140 | 0.006 | 0.147 | |
| writeFastaSC-methods | 0.079 | 0.007 | 0.086 | |
| writeFastaSR-methods | 0.046 | 0.006 | 0.052 | |